https://www.cazypedia.org/api.php?action=feedcontributions&feedformat=atom&user=Ryuichiro+SuzukiCAZypedia - User contributions [en-ca]2026-05-25T13:32:42ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7751Glycoside Hydrolase Family 662012-11-09T06:59:56Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248).<br />
Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs from oral streptococci have been analyzed since 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes show retaining enzymatic properties.<br />
CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.<br />
The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The catalyic nucleophile is aspartic acid and the catalyic acid/base is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (SmDex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex) <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040 <cite>SuzukiR2012</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID [{{PDBlink}}3vmn 3vmn]), in complex with IG3 (PDB ID [{{PDBlink}}3vmo 3vmo]), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID [{{PDBlink}}3vmp 3vmp]), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Staat1974 pmid=4816468<br />
#Hamada1975 pmid=1205620<br />
#Ellis1977 pmid=14177<br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
#Oguma1993 Oguma T, Horiuchi T, and Kobayashi M. ''Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture''. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. http://dx.doi.org/10.1271/bbb.57.1225 <br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7733Glycoside Hydrolase Family 662012-11-08T01:56:45Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012 Igarashi2002</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID 3VMN), in complex with IG3 (PDB ID 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID 3VMP), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Funane2011 pmid=21193067<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7731Glycoside Hydrolase Family 662012-11-08T01:54:24Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012 Igarashi2002</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB ID 3VMN), in complex with IG3 (PDB ID 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB ID 3VMP), have been determined <cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7730Glycoside Hydrolase Family 662012-11-08T01:53:17Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012 Igarashi2002</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB code 3VMN), in complex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP), have been determined<cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7729Glycoside Hydrolase Family 662012-11-08T01:51:57Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012 Igarashi2002</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB code 3VMN), in complex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP), have been determined<cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7728Glycoside Hydrolase Family 662012-11-08T01:49:25Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012 Igarashi2002</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP), have been determined<cite>Nsuzu2012</cite>. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
#SuzukiR2012 pmid=22542750<br />
#Kim2012A pmid=22461618<br />
#Kim2012B pmid=22776355<br />
#Nsuzu2011 pmid=22139161<br />
#Nsuzu2012 pmid=22337884<br />
#Igarashi2002 pmid=12030973<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=User:Ryuichiro_Suzuki&diff=7720User:Ryuichiro Suzuki2012-11-07T15:24:05Z<p>Ryuichiro Suzuki: </p>
<hr />
<div>My name is Ryuichiro Suzuki.<br />
I am an assistant professor at Akita prefectural university in Japan.<br />
I'm now studying starch biosynthesis related enzymes.<br />
Our home page is [[http://www.dbp.akita-pu.ac.jp/~plant-physiol/index.html]].<br />
I contributed to the creation of CAZypedia GH66 page.</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=User:Ryuichiro_Suzuki&diff=7719User:Ryuichiro Suzuki2012-11-07T15:22:41Z<p>Ryuichiro Suzuki: </p>
<hr />
<div>My name is Ryuichiro Suzuki.<br />
I am an assistant professor at Akita prefectural university in Japan.<br />
I'm now studying starch biosynthesis related enzymes.<br />
Our home page is [[http://www.dbp.akita-pu.ac.jp/~plant-physiol/index.html]]<br />
I contributed to the creation of GH66 page.</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7718Glycoside Hydrolase Family 662012-11-07T15:15:03Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (Type I) Dexs, (Type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB code 3VMN), in complex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP), have been determined. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Funane2011 pmid=21193067<br />
Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M. (2011) Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from ''Bacillus circulans'' T-3040. ''Biochim''. ''Biophys''. ''Acta'' '''1814''', 428-434 [DOI: 10.1016/j.bbapap.2010.12.009]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7717Glycoside Hydrolase Family 662012-11-07T15:07:11Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITase from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (type I) Dexs, (type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB code 3VMN), in complex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP), have been determined. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Funane2011 pmid=21193067<br />
Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M. (2011) Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from ''Bacillus circulans'' T-3040. ''Biochim''. ''Biophys''. ''Acta'' '''1814''', 428-434 [DOI: 10.1016/j.bbapap.2010.12.009]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7716Glycoside Hydrolase Family 662012-11-07T15:06:31Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITases from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (type I) Dexs, (type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB code 3VMN), in complex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP), have been determined. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Funane2011 pmid=21193067<br />
Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M. (2011) Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from ''Bacillus circulans'' T-3040. ''Biochim''. ''Biophys''. ''Acta'' '''1814''', 428-434 [DOI: 10.1016/j.bbapap.2010.12.009]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7715Glycoside Hydrolase Family 662012-11-07T15:03:45Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITases from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contains a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (type I) Dexs, (type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB code 3VMN), in complex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP), have been determined. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Funane2011 pmid=21193067<br />
Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M. (2011) Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from ''Bacillus circulans'' T-3040. ''Biochim''. ''Biophys''. ''Acta'' '''1814''', 428-434 [DOI: 10.1016/j.bbapap.2010.12.009]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7714Glycoside Hydrolase Family 662012-11-07T15:01:31Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITases from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contains a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (type I) Dexs, (type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Three structures, ligand free (PDB code 3VMN), in complex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP), have been determined. The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Funane2011 pmid=21193067<br />
Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M. (2011) Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from ''Bacillus circulans'' T-3040. ''Biochim''. ''Biophys''. ''Acta'' '''1814''', 428-434 [DOI: 10.1016/j.bbapap.2010.12.009]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7713Glycoside Hydrolase Family 662012-11-07T14:52:29Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITases from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contains a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (type I) Dexs, (type II) Dexs with low CITase activity, and (Type III) CITases <cite>Kim2012A Kim2012B</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Funane2011 pmid=21193067<br />
Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M. (2011) Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from ''Bacillus circulans'' T-3040. ''Biochim''. ''Biophys''. ''Acta'' '''1814''', 428-434 [DOI: 10.1016/j.bbapap.2010.12.009]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7712Glycoside Hydrolase Family 662012-11-07T14:51:03Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. CITases from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contains a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dexs with low CITase activity, and (iii) CITases <cite>Kim2012A Kim2012B</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Funane2011 pmid=21193067<br />
Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M. (2011) Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from ''Bacillus circulans'' T-3040. ''Biochim''. ''Biophys''. ''Acta'' '''1814''', 428-434 [DOI: 10.1016/j.bbapap.2010.12.009]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7711Glycoside Hydrolase Family 662012-11-07T14:49:10Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite> Normal 0 0 2 false false false EN-US JA X-NONE . CITases from ''Bacillus circulans'' T-3040 (CITase-T3040) produced CI-8 predominantly from dextran, whereas the major product of CITase from ''Paenibacillus'' sp. 598K (CITase-598K) was CI-7 <cite>SuzukiR2012 Funane2011</cite>. CITases contains a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region has been found to be a family 35 carbohydrate-binding module (CBM35) domain that contributes to preference of CI-8 production <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dexs with low CITase activity, and (iii) CITases <cite>Kim2012A Kim2012B</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite> Normal 0 0 2 false false false EN-US JA X-NONE . The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s<sup>-1</sup> and 0.029 mM, respectively <cite>Kim2012B</cite>. Both CITase-T3040 and CITase-598K showed the same ''K''<sub>M</sub> value for dextran 40 (0.18 mM) <cite>SuzukiR2012</cite>. The ''k''<sub>cat</sub> values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s<sup>-1</sup> and 5.8 s<sup>-1</sup>, respectively <cite>SuzukiR2012</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase-T3040, Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase-598K, Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: PsDex by chemical rescue approach <cite>Kim2012A</cite>.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Funane2011 pmid=21193067<br />
Normal 0 0 2 false false false EN-US JA X-NONE Funane, K., Kawabata, Y., Suzuki, R., Kim, Y.M., Kang, H.K., Suzuki, N., Fujimoto, Z., Kimura, A., Kobayashi, M. (2011) Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from ''Bacillus circulans'' T-3040. ''Biochim''. ''Biophys''. ''Acta'' '''1814''', 428-434 [DOI: 10.1016/j.bbapap.2010.12.009]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7710Glycoside Hydrolase Family 662012-11-07T11:05:33Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dexs with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from ''Bacillus circulans'' T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase from ''Paenibacillus'' sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7709Glycoside Hydrolase Family 662012-11-07T10:18:17Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains endo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from ''Bacillus circulans'' T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase from ''Paenibacillus'' sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7706Glycoside Hydrolase Family 662012-11-06T14:26:10Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<sub>8</sub><br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from ''Bacillus circulans'' T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase from ''Paenibacillus'' sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7705Glycoside Hydrolase Family 662012-11-06T14:24:03Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)<br />
<sub>8</sub>|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranase (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze α-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 <cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs <cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>.<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from ''Streptococcus mutans'' (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively <cite>Nsuzu2012</cite>. In Dex from ''Paenibacillus'' sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from ''Bacillus circulans'' T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>. In CITase from ''Paenibacillus'' sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-α-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (β/α)<sub>8</sub>-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of ''Bacillus'' and ''Paenibacillus'' bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. ''Biosci Biotechnol Biochem''. '''72''', 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from ''Paenibacillus'' sp. 598K. ''Biochim''. ''Biophys''. ''Acta'' '''1824''', 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. ''J''. ''Biol''. ''Chem''. '''287''', 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. ''FEBS J''. '''279''', 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from ''Streptococcus mutans''. ''Acta Crystallogr''. ''F Struct''. ''Biol''. ''Cryst''. ''Commun''. '''67''', 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by ''Streptococcus mutans'' dextranase belonging to glycoside hydrolase family 66. ''J''. ''Biol''. ''Chem''. '''287''', 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7704Glycoside Hydrolase Family 662012-11-06T10:18:07Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A Nsuzu2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta 1824, 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7703Glycoside Hydrolase Family 662012-11-06T10:16:37Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzukiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta 1824, 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7702Glycoside Hydrolase Family 662012-11-06T10:15:32Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzkiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta 1824, 919-924 [DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7701Glycoside Hydrolase Family 662012-11-06T10:14:41Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzkiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta 1824, 919-924 [ DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7700Glycoside Hydrolase Family 662012-11-06T10:13:14Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzkiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta 1824, 919-924 Normal 0 0 2 false false false EN-US JA X-NONE [ DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7699Glycoside Hydrolase Family 662012-11-06T10:10:29Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzkiR2012 pmid=22542750<br />
Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta [ DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
<biblio><br />
#Nsuzu2012 pmid=22337884<br />
Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio> <br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7698Glycoside Hydrolase Family 662012-11-06T10:05:07Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
# 1. Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzkiR2012 pmid=22542750<br />
# 2. Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta [ DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
# 3. Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
# 4. Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
# 5. Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22337884<br />
# 6. Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7697Glycoside Hydrolase Family 662012-11-06T10:02:40Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases.<br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
# 1. Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [https://www.jstage.jst.go.jp/article/bbb/72/12/72_80384/_pdf DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzkiR2012 pmid=22542750<br />
# 2. Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta [http://www.sciencedirect.com/science/article/pii/S1570963912000635 DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
# 3. Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [http://www.jbc.org/content/287/24/19927.long DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=22776355<br />
# 4. Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [DOI: 10.1111/j.1742-4658.2012.08698.x]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22139161<br />
# 5. Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [DOI: 10.1107/S1744309111038425]<br />
</biblio><br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=22337884<br />
# 6. Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [DOI: 10.1074/jbc.M112.342444]<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7696Glycoside Hydrolase Family 662012-11-06T08:48:31Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17<cite>Funane2008</cite>. CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>. Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases. <br />
<br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination:.<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=19060390<br />
# 1. Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. [https://www.jstage.jst.go.jp/article/bbb/72/12/72_80384/_pdf DOI: 10.1271/bbb.80384]<br />
</biblio><br />
<biblio><br />
#SuzkiR2012 pmid=22542750<br />
# 2. Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta [http://www.sciencedirect.com/science/article/pii/S1570963912000635 DOI: 10.1016/j.bbapap.2012.04.001]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=22461618<br />
# 3. Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 [http://www.jbc.org/content/287/24/19927.long DOI: 10.1074/jbc.M111.339036]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=<br />
# 4. Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 [http: DOI: ]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=<br />
# 5. Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 [http: DOI: ]<br />
</biblio><br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=<br />
# 6. Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. [http: DOI: ]<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_66&diff=7695Glycoside Hydrolase Family 662012-11-06T06:28:48Z<p>Ryuichiro Suzuki: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ryuichiro Suzuki^^^<br />
* [[Responsible Curator]]: ^^^Zui Fujimoto^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH66'''<br />
|-<br />
|'''Clan''' <br />
|none, (β/α)8<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH66.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Glycoside hydrolases of GH66 contains exo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC 2.4.1.248). Dexs hydrolyze a-1,6 linkage of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dexs are classified into GH49 and GH66. In contrast to inverting GH49 enzymes, GH66 enzymes are retaining enzymes. CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 Normal 0 0 2 false false false EN-US JA X-NONE <cite>Funane2008</cite>. Normal 0 0 2 false false false EN-US JA X-NONE<br />
<br />
CITases produce CIs from IG4 and larger IGs<cite>SuzukiR2012</cite>.<br />
<br />
Some Dexs displaying strong dextranolytic activity and low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>. The GH66 enzymes are classified into the following three types: (i) Dexs, (ii) Dex with low CITase activity, and (iii) CITases.<br />
<br />
Normal 0 0 2 false false false EN-US JA X-NONE <br />
== Kinetics and Mechanism ==<br />
GH66 enzymes are retaining enzymes, as first shown by structural <cite>Nsuzu2011 Nsuzu2012</cite>and chemical rescue studies <cite>Kim2012A</cite>. .<br />
== Catalytic Residues ==<br />
To date, catalytic residues of four GH66 enzymes were identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012</cite>. In Dex from Streptococcus mutans (SmDex), Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively<cite>Nsuzu2012</cite>. In Dex from Paenibacillus sp. (PsDex), Asp340 and Glu412 are nucleophile and acid/base catalyst, respectively <cite>Kim2012A</cite>. In CITase from Bacillus circulans T-3040 (CITase-T3040), Asp270 and Glu342 are nucleophile and acid/base catalyst, respectively<cite>SuzukiR2012</cite>. In CITase from Paenibacillus sp. 598K (CITase-598K), Asp269 and Glu341 are nucleophile and acid/base catalyst, respectively <cite>SuzukiR2012</cite>.<br />
== Three-dimensional structures ==<br />
The crystal structures of truncated mutant of SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of GH66 enzymes <cite>Nsuzu2011 Nsuzu2012</cite>. Ligand free (PDB code 3VMN), in compex with IG3 (PDB code 3VMO), and in complex with 4’,5’-epoxypentyl-a-D-glucopyranoside (PDB code 3VMP). The catalytic domain of the enzyme is a (b/a)8-barrel fold. The enzyme consists of at least three domains.<br />
== Family Firsts ==<br />
;First stereochemistry determination: Normal 0 0 2 false false false EN-US JA X-NONE .<br />
;First catalytic nucleophile identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite> Normal 0 0 2 false false false EN-US JA X-NONE .<br />
;First general acid/base residue identification: SmDex and PsDex by structural study and chemical rescue approach, respectively <cite>Kim2012A SuzukiR2012</cite>.<br />
;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2011 Nsuzu2012</cite> .<br />
<br />
== References ==<br />
<biblio><br />
#Funane2008 pmid=<br />
# 1. Funane K, Terasawa K, Mizuno Y, Ono H, Gibu S, Tokashiki T, Kawabata Y, Kim YM, Kimura A, Kobayashi M.(2008) Isolation of Bacillus and Paenibacillus bacterial strains that produce large molecules of cyclic isomaltooligosaccharides. Biosci Biotechnol Biochem. 72, 3277-3280. Normal 0 0 2 false false false EN-US JA X-NONE [http: DOI: ]<br />
</biblio><br />
<biblio><br />
#SuzkiR2012 pmid=<br />
# 2. Suzuki, R., Terasawa, K., Kimura, K., Fujimoto, Z., Momma, M., Kobayashi, M., Kimura, A., and Funane, K. (2012) Biochemical characterization of a novel cycloisomaltooligosaccharide glucanotransferase from Paenibacillus sp. 598K. Biochim. Biophys. Acta Normal 0 0 2 false false false EN-US JA X-NONE [http: DOI: ]<br />
</biblio><br />
<biblio><br />
#Kim2012A pmid=<br />
# 3. Kim, Y. M., Kiso, Y., Muraki, T., Kan, M. S., Nakai, H., Saburi, W., Lang, W., Kang, H. K., Okuyama, M., Mori, H., Suzuki, R., Funane, K., Suzuki, N., Momma, M., Fujimoto, Z., Oguma, T., Kobayashi, M., Kim, D., and Kimura, A. (2012) Novel dextranase catalyzing cycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. J. Biol. Chem. 287, 19927-19935 Normal 0 0 2 false false false EN-US JA X-NONE [http: DOI: ]<br />
</biblio><br />
<biblio><br />
#Kim2012B pmid=<br />
# 4. Kim, YM, Yamamoto, E, Kang, MS, Nakai, H, Saburi, W, Okuyama, M, Mori, H, Funane, K, Momma, M, Fujimoto, Z, Kobayashi, M, Kim, D and Kimura, A (2012) Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions. FEBS J. 279, 3185-3191 Normal 0 0 2 false false false EN-US JA X-NONE [http: DOI: ]<br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=<br />
# 5. Suzuki, N., Kim, Y. M., Fujimoto, Z., Momma, M., Kang, H. K., Funane, K., Okuyama, M., Mori, H., and Kimura, A. (2011) Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 67, 1542–1544 Normal 0 0 2 false false false EN-US JA X-NONE [http: DOI: ]<br />
</biblio><br />
</biblio><br />
<biblio><br />
#Nsuzu2011 pmid=<br />
# 6. Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K & Kimura A (2012) Structural elucidation of dextran degradation mechanism by Streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem 287, 19916-19926. Normal 0 0 2 false false false EN-US JA X-NONE [http: DOI: ]<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH066]]</div>Ryuichiro Suzukihttps://www.cazypedia.org/index.php?title=User:Ryuichiro_Suzuki&diff=7691User:Ryuichiro Suzuki2012-11-05T16:35:56Z<p>Ryuichiro Suzuki: Created page with "Test. My name is Ryuichiro Suzuki. I am an assistant professor at Akita prefectural university in Japan. I'm now studying starch biosynthesis related enzymes. Our home page is..."</p>
<hr />
<div>Test.<br />
My name is Ryuichiro Suzuki.<br />
I am an assistant professor at Akita prefectural university in Japan.<br />
I'm now studying starch biosynthesis related enzymes.<br />
Our home page is [[http://www.dbp.akita-pu.ac.jp/~plant-physiol/index.html]]</div>Ryuichiro Suzuki