Glycoside Hydrolase Family 66 - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:18:01Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Spencer Williams: /* Three-dimensional structures */

2017-09-07T00:33:42Z

Three-dimensional structures

Spencer Williams at 00:31, 7 September 2017

2017-09-07T00:31:44Z

Spencer Williams at 00:25, 7 September 2017

2017-09-07T00:25:31Z

Spencer Williams at 00:20, 7 September 2017

2017-09-07T00:20:25Z

Spencer Williams at 00:20, 7 September 2017

2017-09-07T00:20:01Z

Spencer Williams at 00:13, 7 September 2017

2017-09-07T00:13:46Z

Spencer Williams at 00:11, 7 September 2017

2017-09-07T00:11:24Z

Spencer Williams at 00:09, 7 September 2017

2017-09-07T00:09:47Z

Harry Brumer at 03:44, 1 September 2017

2017-09-01T03:44:05Z

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 {{CuratorApproved}}
-* [[Author]]: ^^^Ryuichiro Suzuki^^^
+* [[Author]]: [[User:Ryuichiro Suzuki|Ryuichiro Suzuki]]
-* [[Responsible Curator]]:  ^^^Zui Fujimoto^^^
+* [[Responsible Curator]]:  [[User:Zui Fujimoto|Zui Fujimoto]]
 ----

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 Crystal structures of a truncated mutant of ''Streptococcus mutans'' ''Sm''Dex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of a GH66 enzyme <cite>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 solved <cite>Nsuzu2012</cite>. The catalytic domain of ''Sm''Dex 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.
-A structure for a GH66 CITase-T3040 (PDB ID [{{PDBlink}}3wnk 3wnk]-[{{PDBlink}}3wno 3wno]) has been reported <cite>Nsuzu2014</cite>. CITase-T3040 has a similar domain arrangement to that of ''Sm''Dex, but one [[CBM35]] domain is inserted into the catalytic module, and assist the substrate uptake and dominant CI-8 production.
+A structure for a GH66 CITase-T3040 (PDB ID [{{PDBlink}}3wnk 3wnk]-[{{PDBlink}}3wno 3wno]) has been reported <cite>Nsuzu2014</cite>. CITase-T3040 has a similar domain arrangement to that of ''Sm''Dex, but a [[CBM35]] domain is inserted into the catalytic module, which assists substrate uptake and production of the dominant cyclooctylisomaltoside (CI-8).
 == Family Firsts ==

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 == Family Firsts ==
-;First stereochemistry determination: ''Bacillus'' sp. T-3040 CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.
+;First stereochemistry determination: ''Bacillus'' sp. T-3040 CITase-T3040 by structural analysis of transglycosylation products using <sup>1</sup>H-NMR and <sup>13</sup>C-NMR spectroscopy <cite>Oguma1993</cite>.
 ;First [[catalytic nucleophile]] identification: ''Streptococcus mutans'' ''Sm''Dex and ''Paenibacillus'' sp. ''Ps''Dex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
 ;First [[general acid/base]] residue identification: ''Sm''Dex and ''Ps''Dex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.

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 Dex enzymes hydrolyze α-1,6-linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been studied since the 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into families [[GH49]] and GH66.
-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 is a family 35 carbohydrate-binding module ([[CBM35]]) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.
+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'' sp. 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 is a family 35 carbohydrate-binding module ([[CBM35]]) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.
 == Kinetics and Mechanism ==
-GH66 enzymes are [[retaining]] enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]]. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (''Bt''Dex) 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>. Dexs from family [[GH49]] are inverting enzymes.
+GH66 enzymes are [[retaining]] enzymes, as first shown by structural analysis of cyclic dextrins formed by transglycosylation from a-1,6-glucan by ''Bacillus'' sp. T-3040 CITase-T3040 <cite>Oguma1993</cite>. This has been supported by subsequent structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]]. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (''Bt''Dex) 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>. Dexs from family [[GH49]] are inverting enzymes.
 == Catalytic Residues ==
@@ Line 48: / Line 48: @@
 == Family Firsts ==
-;First stereochemistry determination: ''Bacillus circulans'' T-3040 CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.
+;First stereochemistry determination: ''Bacillus'' sp. T-3040 CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.
 ;First [[catalytic nucleophile]] identification: ''Streptococcus mutans'' ''Sm''Dex and ''Paenibacillus'' sp. ''Ps''Dex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
 ;First [[general acid/base]] residue identification: ''Sm''Dex and ''Ps''Dex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.

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 Family 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>.
-Dex enzymes hydrolyze α-1,6-linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been studied since the 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into [[GH49]] and GH66.
+Dex enzymes hydrolyze α-1,6-linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been studied since the 1970s <cite>Staat1974 Hamada1975 Ellis1977</cite>. Dexs are classified into families [[GH49]] and GH66.
 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 is a family 35 carbohydrate-binding module ([[CBM35]]) domain <cite>Funane2011</cite>. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered <cite>Kim2012A Kim2012B</cite>.

@@ Line 40: / Line 40: @@
 == Catalytic Residues ==
-Catalytic residues of several GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general acid/base]] is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (''Sm''Dex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (PsDex)  <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040  <cite>SuzukiR2012, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K  <cite>SuzukiR2012</cite>.
+Catalytic residues of several GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general acid/base]] is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from ''Streptococcus mutans'' (''Sm''Dex) <cite>Nsuzu2012 Igarashi2002</cite>, Asp340 and Glu412 in Dex from ''Paenibacillus'' sp. (''Ps''Dex)  <cite>Kim2012A</cite>, Asp270 and Glu342 in CITase-T3040  <cite>SuzukiR2012, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K <cite>SuzukiR2012</cite>.
 == Three-dimensional structures ==
@@ Line 48: / Line 48: @@
 == Family Firsts ==
-;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.
+;First stereochemistry determination: ''Paenibacillus'' sp. 598K CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.
-;First [[catalytic nucleophile]] identification: ''Streptococcus mutans'' ''Sm''Dex and ''Ps''Dex by structural study  <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
+;First [[catalytic nucleophile]] identification: ''Streptococcus mutans'' ''Sm''Dex and ''Paenibacillus'' sp. ''Ps''Dex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
-;First [[general acid/base]] residue identification: ''Sm''Dex and ''Ps''Dex by structural study  <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
+;First [[general acid/base]] residue identification: ''Sm''Dex and ''Ps''Dex by structural study <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
-;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2012</cite> .
+;First 3-D structure: Truncated mutant of ''Sm''Dex <cite>Nsuzu2012</cite>.
 == References ==

@@ Line 28: / Line 28: @@
 == Substrate specificities ==
-[[Glycoside hydrolases]] of GH66 contains [[endo]]-acting dextranase (Dex; EC [{{EClink}}3.2.1.11 3.2.1.11]) and cycloisomaltooligosaccharide glucanotransferase (CITase; EC [{{EClink}}2.4.1.248 2.4.1.248]).
+[[Glycoside hydrolases]] of family GH66 include [[endo]]-acting dextranases (Dex; EC [{{EClink}}3.2.1.11 3.2.1.11]) and cycloisomaltooligosaccharide glucanotransferases (CITase; EC [{{EClink}}2.4.1.248 2.4.1.248]).
-Dex enzymes hydrolyze α-1,6 linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes 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 use a [[classical Koshland retaining mechanism]].
+Family 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>.
 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 is a family 35 carbohydrate-binding module ([[CBM35]]) domain <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>.
 == Kinetics and Mechanism ==
-GH66 enzymes are [[retaining]] enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]]. 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>.
+GH66 enzymes are [[retaining]] enzymes, as first shown by structural <cite>Nsuzu2012</cite> and chemical rescue studies <cite>Kim2012A</cite>. GH66 enzymes appear to operate through a [[classical Koshland retaining mechanism]]. The ''k''<sub>cat</sub> and ''K''<sub>M</sub> values of Dex from ''Bacteroides thetaiotaomicron'' VPI-5482 (''Bt''Dex) 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>. Dexs from family [[GH49]] are inverting enzymes.
 == Catalytic Residues ==
-To date, catalytic residues of four GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general 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, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K  <cite>SuzukiR2012</cite>.
+Catalytic residues of several GH66 enzymes have been identified by mutational and structural studies <cite>SuzukiR2012 Kim2012A Nsuzu2012 Igarashi2002</cite>. The [[catalytic nucleophile]] is aspartic acid and the [[general 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, Nsuzu2014</cite>, and Asp269 and Glu341 in CITase-598K  <cite>SuzukiR2012</cite>.
 == Three-dimensional structures ==
-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>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.
+Crystal structures of a truncated mutant of ''Sm''Dex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of a GH66 enzyme <cite>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 solved <cite>Nsuzu2012</cite>. The catalytic domain of ''Sm''Dex 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.
-The second structure for GH66 has been reported for CITase-T3040 (PDB ID [{{PDBlink}}3wnk 3wnk]-[{{PDBlink}}3wno 3wno])<cite>Nsuzu2014</cite>. CITase-T3040 has a similar domain arrangement to that of SmDex, but one [[CBM35]] domain is inserted into the catalytic module, and assist the substrate uptake and dominant CI-8 production.
+A structure for a GH66 CITase-T3040 (PDB ID [{{PDBlink}}3wnk 3wnk]-[{{PDBlink}}3wno 3wno]) has been reported <cite>Nsuzu2014</cite>. CITase-T3040 has a similar domain arrangement to that of ''Sm''Dex, but one [[CBM35]] domain is inserted into the catalytic module, and assist the substrate uptake and dominant CI-8 production.
 == Family Firsts ==
 ;First stereochemistry determination: CITase-T3040 using <sup>1</sup>H-NMR, <sup>13</sup>C-NMR, and IR spectra <cite>Oguma1993</cite>.
-;First [[catalytic nucleophile]] identification: SmDex and PsDex by structural study  <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
+;First [[catalytic nucleophile]] identification: ''Sm''Dex and ''Ps''Dex by structural study  <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
-;First [[general acid/base]] residue identification: SmDex and PsDex by structural study  <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
+;First [[general acid/base]] residue identification: ''Sm''Dex and ''Ps''Dex by structural study  <cite>Nsuzu2012</cite> and chemical rescue approach <cite>Kim2012A</cite>, respectively.
 ;First 3-D structure: Truncated mutant of SmDex <cite>Nsuzu2012</cite> .