CAZypedia - User contributions [en-ca]

Carbohydrate Binding Module Family 83

2019-05-09T16:45:27Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 82

2019-05-09T16:44:09Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-10T20:05:48Z

Nicole Koropatkin:

{{CuratorApproved}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==
[[File:SusG_Cazy.png|thumb|400px|left|'''Figure 1: ''B. thetaiotaomicron'' SusG.''' Cartoon representation of the crystal structure of the catalytically inactive SusG D498N mutant complexed with maltoheptaose (PDB 3K8L). The structure is colored blue to red from the N- to C-terminus. The CBM58, active site and surface starch binding site are labeled. The CBM58 occupies residues 216-335. ]]
Only a single CBM58 family member has been characterized, the founding member from the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' (Figure 1) <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose, a pseudotetrasaccharide amylase inhibitor. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM <cite>Koropatkin2010</cite>. Based upon these data, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch.

== Structural Features ==
The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α-glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 2: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing [[GH13]] enzymes as listed in the [http://www.cazy.org/CBM58.html CAZy database]. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]A unique facet of the CBM58 of SusG is its position in the middle of the [[GH13]] amylase fold, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic B domain (residues 153-215 and 336-363), and essentially expands the typically small B domain of GH13 enzymes. Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the B domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position <cite>Koropatkin2010</cite>. The CBM58 family is small, with the seminal members all arising from the Bacteroidetes phylum. This includes similar [[GH13]] enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of 15 representative [[GH13]] enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain (Figure 2). The majority of these CBM58-containing proteins are expressed within canonical polysaccharide utilization loci <cite>Foley2016 Grondin2017</cite> of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

== Functionalities ==
CBM58 is only found within [[GH13]] enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grows the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

The CBM58 of SusG has been replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>. In these experiments, the SusG-halo fusion partitioned between mobile and confined populations on the cell surface during growth on glucose and starch respectively, and the diffusion coefficient of the protein was measurably slower when interacting with starch granules, and in the presence of the other Sus surface proteins <cite>Karunatilaka2014</cite>.

== Family Firsts ==
;First Identified: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron'' <cite>Koropatkin2010</cite>.

;First Structural Characterization: The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides <cite>Koropatkin2010</cite>.

== References ==
<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179
#Foley2016 pmid=27137179
#Grondin2017 pmid=28138099
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-10T20:03:34Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==
[[File:SusG_Cazy.png|thumb|400px|left|'''Figure 1: ''B. thetaiotaomicron'' SusG.''' Cartoon representation of the crystal structure of the catalytically inactive SusG D498N mutant complexed with maltoheptaose (PDB 3K8L). The structure is colored blue to red from the N- to C-terminus. The CBM58, active site and surface starch binding site are labeled. The CBM58 occupies residues 216-335. ]]
Only a single CBM58 family member has been characterized, the founding member from the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' (Figure 1) <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose, a pseudotetrasaccharide amylase inhibitor. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM <cite>Koropatkin2010</cite>. Based upon these data, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch.

== Structural Features ==
The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α-glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 2: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing [[GH13]] enzymes as listed in the [http://www.cazy.org/CBM58.html CAZy database]. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]A unique facet of the CBM58 of SusG is its position in the middle of the [[GH13]] amylase fold, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic B domain (residues 153-215 and 336-363), and essentially expands the typically small B domain of GH13 enzymes. Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the B domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position <cite>Koropatkin2010</cite>. The CBM58 family is small, with the seminal members all arising from the Bacteroidetes phylum. This includes similar [[GH13]] enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of 15 representative [[GH13]] enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain (Figure 2). The majority of these CBM58-containing proteins are expressed within canonical polysaccharide utilization loci <cite>Foley2016 Grondin2017</cite> of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

== Functionalities ==
CBM58 is only found within [[GH13]] enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grows the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

The CBM58 of SusG has been replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>. In these experiments, the SusG-halo fusion partitioned between mobile and confined populations on the cell surface during growth on glucose and starch respectively, and the diffusion coefficient of the protein was measurably slower when interacting with starch granules, and in the presence of the other Sus surface proteins <cite>Karunatilaka2014</cite>.

== Family Firsts ==
;First Identified: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron'' <cite>Koropatkin2010</cite>.

;First Structural Characterization: The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides <cite>Koropatkin2010</cite>.

== References ==
<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179
#Foley2016 pmid=27137179
#Grondin2017 pmid=28138099
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-10T20:02:13Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==
[[File:SusG_Cazy.png|thumb|400px|left|'''Figure 1: ''B. thetaiotaomicron'' SusG.''' Cartoon representation of the crystal structure of the catlytically inactive SusG D498N mutant complexed with maltoheptaose (PDB 3K8L). The structure is colored blue to red from the N- to C-terminus. The CBM58, active site and surface starch binding site are labeled. The CBM58 occupies residues 216-335. ]]
Only a single CBM58 family member has been characterized, the founding member from the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' (Figure 1) <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose, a pseudotetrasaccharide amylase inhibitor. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM <cite>Koropatkin2010</cite>. Based upon these data, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch.

== Structural Features ==
The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α-glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 2: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing [[GH13]] enzymes as listed in the [http://www.cazy.org/CBM58.html CAZy database]. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]A unique facet of the CBM58 of SusG is its position in the middle of the [[GH13]] amylase fold, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic B domain (residues 153-215 and 336-363), and essentially expands the typically small B domain of GH13 enzymes. Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the B domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position <cite>Koropatkin2010</cite>. The CBM58 family is small, with the seminal members all arising from the Bacteroidetes phylum. This includes similar [[GH13]] enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of 15 representative [[GH13]] enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain (Figure 2). The majority of these CBM58-containing proteins are expressed within canonical polysaccharide utilization loci <cite>Foley2016 Grondin2017</cite> of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

== Functionalities ==
CBM58 is only found within [[GH13]] enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grows the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

The CBM58 of SusG has been replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>. In these experiments, the SusG-halo fusion partitioned between mobile and confined populations on the cell surface during growth on glucose and starch respectively, and the diffusion coefficient of the protein was measurably slower when interacting with starch granules, and in the presence of the other Sus surface proteins <cite>Karunatilaka2014</cite>.

== Family Firsts ==
;First Identified: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron'' <cite>Koropatkin2010</cite>.

;First Structural Characterization: The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides <cite>Koropatkin2010</cite>.

== References ==
<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179
#Foley2016 pmid=27137179
#Grondin2017 pmid=28138099
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-10T20:01:26Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==
[[File:SusG_Cazy.png|thumb|400px|left|'''Figure 1: ''B. thetaiotaomicron'' SusG.''' Cartoon representation of the crystal structure of the catlytically inactive SusG D498N mutant complexed with maltoheptaose (PDB 3K8L). The structure is colored blue to red from the N- to C-terminus. The CBM58, active site and surface starch binding site are labeled. The CBM58 occupies residues 216-335. ]]
Only a single CBM58 family member has been characterized, the founding member from the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose, a pseudotetrasaccharide amylase inhibitor. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM <cite>Koropatkin2010</cite>. Based upon these data, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch.

== Structural Features ==
The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α-glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 2: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing [[GH13]] enzymes as listed in the [http://www.cazy.org/CBM58.html CAZy database]. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]A unique facet of the CBM58 of SusG is its position in the middle of the [[GH13]] amylase fold, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic B domain (residues 153-215 and 336-363), and essentially expands the typically small B domain of GH13 enzymes. Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the B domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position <cite>Koropatkin2010</cite>. The CBM58 family is small, with the seminal members all arising from the Bacteroidetes phylum. This includes similar [[GH13]] enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of 15 representative [[GH13]] enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain (Figure 2). The majority of these CBM58-containing proteins are expressed within canonical polysaccharide utilization loci <cite>Foley2016 Grondin2017</cite> of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

== Functionalities ==
CBM58 is only found within [[GH13]] enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grows the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

The CBM58 of SusG has been replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>. In these experiments, the SusG-halo fusion partitioned between mobile and confined populations on the cell surface during growth on glucose and starch respectively, and the diffusion coefficient of the protein was measurably slower when interacting with starch granules, and in the presence of the other Sus surface proteins <cite>Karunatilaka2014</cite>.

== Family Firsts ==
;First Identified: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron'' <cite>Koropatkin2010</cite>.

;First Structural Characterization: The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides <cite>Koropatkin2010</cite>.

== References ==
<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179
#Foley2016 pmid=27137179
#Grondin2017 pmid=28138099
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

File:SusG Cazy.png

2017-09-10T19:53:28Z

Nicole Koropatkin: Nicole Koropatkin uploaded a new version of File:SusG Cazy.png

File:SusG Cazy.png

2017-09-10T19:48:40Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-07T18:56:19Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose, a pseudotetrasaccharide amylase inhibitor. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the amylase fold, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic B domain (residues 153-215 and 336-363), and essentially expands the typically small B domain of GH13 enzymes. Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the B domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain (Figure 1). The majority of these CBM58-containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 1: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing GH13 enzymes as listed in www.cazy.org/CBM58.html. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grows the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>. In these experiments, the SusG-halo fusion partitioned between mobile and confined populations on the cell surface during growth on glucose and starch respectively, and the diffusion coefficient of the protein was measurably slower when interacting with starch granules, and in the presence of the other Sus surface proteins <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron'' <cite>Koropatkin2010</cite>.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides <cite>Koropatkin2010</cite>.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-07T18:55:46Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose, a pseudotetrasaccharide amylase inhibitor. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the amylase fold, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic B domain (residues 153-215 and 336-363), and essentially expands the typically small B domain of GH13 enzymes. Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the B domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain (Figure 1). The majority of these CBM58-containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 1: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing GH13 enzymes as listed in www.cazy.org/CBM58.html. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grows the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>. In these experiments, the SusG-halo fusion partitioned between mobile and confined populations on the cell surface during growth on glucose and starch respectively, and the diffusion coefficient of the protein was measurably slower when interacting with starch granules, and in the presence of the other Sus surface proteins <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron'' ''<cite>Koropatkin2010</cite>''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides <cite>Koropatkin2010</cite>.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-07T18:49:15Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose, a pseudotetrasaccharide amylase inhibitor. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the catalytic domain polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic B domain (residues 153-215 and 336-363), and essentially expands the typically small B domain of GH13 enzymes. Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the B domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 1: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing GH13 enzymes as listed in www.cazy.org/CBM58.html. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>. In these experiments, the SusG-halo fusion partitioned between mobile and confined populations on the cell surface during growth on glucose and starch respectively, and the diffusion coefficient of the protein was measurably slower when interacting with starch granules, and in the presence of the other Sus surface proteins <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron'' ''<cite>Koropatkin2010</cite>''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides <cite>Koropatkin2010</cite>.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-07T18:45:54Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose, a pseudotetrasaccharide amylase inhibitor. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the catalytic domain polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic B domain (residues 153-215 and 336-363), and essentially expands the typically small B domain of GH13 enzymes. Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the B domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 1: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing GH13 enzymes as listed in www.cazy.org/CBM58.html. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>. In these experiments, the SusG-halo fusion partitioned between mobile and confined populations on the cell surface during growth on glucose and starch respectively, and the diffusion coefficient of the protein was measurably slower when interacting with starch granules, and in the presence of the other Sus surface proteins <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-07T18:11:14Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the catalytic domain polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 1: CBM58 sequence alignment.''' Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). All protein names (left) refer to the locus tags of CBM58-containing GH13 enzymes as listed in www.cazy.org/CBM58.html. The numbering to the right refers to the amino acid position of each protein. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. ]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-07T18:06:19Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the catalytic domain polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58-2.png|thumb|400px|right|'''Figure 1: CBM58 sequence alignment.''' Amino acid sequence alignment using CLUSTALW in Megalign (DNASTAR, Madison, WI). All protein names at the left refer to locus names as designated at www.cazy.org/CBM58.html. The numbering to the right refers to the amino acid sequence, and displays the CBM58 region of the relevant enzymes including some of the surrounding sequence. For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335. ]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-07T18:00:53Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the catalytic domain polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58-2.png|thumb|300px|right|'''Figure 1.''' This is the legend?.]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-07T18:00:23Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the catalytic domain polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58-2.png|thumb|300px|right|'''Figure X.''' Figure legend.]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

File:CBM58-2.png

2017-09-07T17:59:20Z

Nicole Koropatkin:

File:CBM58.pdf

2017-09-07T17:57:04Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-07T17:56:35Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan is cradled by aromatic stacking interactions with two SusG CBM58 aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the catalytic domain polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'', ''Alistipes shahii'', ''Bacteroides dorei'', ''Bacteroides eggerthii'' and ''Bacteroides vulgatus''. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

[[File:CBM58.pdf|thumb|300px|right|'''Figure X.''' Figure legend.]]

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is unusual as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

File:CBM58a align nmk.pdf

2017-09-07T17:53:35Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-06T19:12:10Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan at CBM58 in SusG is cradled by aromatic stacking interactions with two aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'' ''Alistipes shahii'' ''Bacteroides dorei'' ''Bacteroides eggerthii'' and ''Bacteroides vulgatus'' A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is somewhat unique as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka2014</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-06T19:11:42Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan at CBM58 in SusG is cradled by aromatic stacking interactions with two aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'' ''Alistipes shahii'' ''Bacteroides dorei'' ''Bacteroides eggerthii'' and ''Bacteroides vulgatus'' A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is somewhat unique as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179

</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-06T19:10:31Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan at CBM58 in SusG is cradled by aromatic stacking interactions with two aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues that stack with the tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes similar GH13 enzymes from isolates of ''Alistipes finegoldii'' ''Alistipes shahii'' ''Bacteroides dorei'' ''Bacteroides eggerthii'' and ''Bacteroides vulgatus'' A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is somewhat unique as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live ''B. thetaiotaomicron'' cultured on glucose and starch <cite>Karunatilaka</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179
0 0 1 1 8 University of Michigan Medical School 1 1 8 14.0
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-06T18:57:12Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed binding to maltoheptaose as well as acarbose. Isothermal titration calorimetry as well as affinity PAGE demonstrates that the CBM58 of SusG binds maltoheptaose, α-cyclodextrin and amylopectin. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, connecting β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan at CBM58 in SusG is cradled by aromatic stacking interactions with two aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues stacking with the two tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain the, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338 span about 12Å between the A domain and the CBM58 have B-factors and an amino acid sequence imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum and include similar GH13 enzymes from isolates of ''Alistipes finegoldii'' ''Alistipes shahii'' ''Bacteroides dorei'' ''Bacteroides eggerthii'' and ''Bacteroides vulgatus'' A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain.

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is somewhat unique as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live B. thetaiotaomicron cultured on glucose and starch <cite>Karunatilaka</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain as CBM58 that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179
0 0 1 1 8 University of Michigan Medical School 1 1 8 14.0
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-06T18:49:25Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed binding to maltoheptaose as well as acarbose. Isothermal titration calorimetry as well as affinity PAGE demonstrates that the CBM58 of SusG binds maltoheptaose, α-cyclodextrin and amylopectin. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, connecting β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan at CBM58 in SusG is cradled by aromatic stacking interactions with two aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues stacking with the two tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain the, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338 span about 12Å between the A domain and the CBM58 have B-factors and an amino acid sequence imply this domain is held in a fixed position, without inherent flexibility <cite>Koropatkin2010</cite>. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum and include similar GH13 enzymes from isolates of ''Alistipes finegoldii'' ''Alistipes shahii'' ''Bacteroides dorei'' ''Bacteroides eggerthii'' and ''Bacteroides vulgatus'' A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain.

== Functionalities ==

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the ''B. thetaiotaomicron'' SusG and like enzymes is somewhat unique as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å and on the opposite face of the protein from the catalytic cleft <cite>Koropatkin2010</cite>. A mutant of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme <cite>Koropatkin2010</cite>. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~40% of the wild-type activity on insoluble corn starch <cite>Koropatkin2010</cite>. ''B. thetaiotaomicron'' expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches <cite>Cameron2014</cite>.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live B. thetaiotaomicron cultured on glucose and starch <cite>Karunatilaka</cite>.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from ''B. thetaiotaomicron''.

; First Structural Characterization
:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain as CBM58 that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
#Cameron2014 pmid=25205092
#Karunatilaka2014 pmid=25389179
0 0 1 1 8 University of Michigan Medical School 1 1 8 14.0
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-09-06T18:43:20Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont ''Bacteroides thetaiotaomicron'' <cite>Koropatkin2010</cite>. The crystal structure of SusG featuring CBM58 revealed binding to maltoheptaose as well as acarbose. Isothermal titration calorimetry as well as affinity PAGE demonstrates that the CBM58 of SusG binds maltoheptaose, α-cyclodextrin and amylopectin. Based upon these data as reported by Koropatkin<cite>Koropatkin2010</cite>, the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

== Structural Features ==

The crystal structure of CBM58 from SusG of ''B. thetaiotaomicron'' displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, connecting β6 and β7, and β7 and β8 <cite>Koropatkin2010</cite>. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM <cite>Gilbert2013</cite>. Like many starch-specific CBMs <cite>Machovic2006</cite>, the helical α -glucan at CBM58 in SusG is cradled by aromatic stacking interactions with two aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues stacking with the two tryptophans <cite>Koropatkin2010</cite>.

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain the, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338 span about 12Å between the A domain and the CBM58 have B-factors and an amino acid sequence imply this domain is held in a fixed position, without inherent flexibility. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum and include similar GH13 enzymes from isolates of Alistipes finegoldii, Alistipes shahii, Bacteroides dorei, Bacteroides eggerthii, and Bacteroides vulgatus. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain.

== Functionalities ==

0 0 1 156 910 University of Michigan Medical School 14 5 1061 14.0

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the B. thetaiotaomicron SusG and like enzymes is somewhat unique as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å and on the opposite face of the protein from the catalytic cleft. A mutant of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~40% of the wild-type activity on insoluble corn starch. B. thetaiotaomicron expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches.

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live B. thetaiotaomicron cultured on glucose and starch.

== Family Firsts ==

; First Identified
: The CBM58 domain was identified during the biochemical and structural characterization of SusG from B. thetaiotaomicron.

; First Structural Characterization

:The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain as CBM58 that recognizes starch and maltooligosaccharides.

== References ==

<biblio>
#Koropatkin2010 pmid=20159465
#Gilbert2013 pmid=23769966
#Machovic2006 pmid=17013558
# DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
# Boraston2004 pmid=15214846
# Hashimoto2006 pmid=17131061
# Shoseyov2006 pmid=16760304
# Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM058]]

User:Nicole Koropatkin

2017-09-06T14:08:25Z

Nicole Koropatkin:

User:Nicole Koropatkin

2017-09-06T14:08:08Z

Nicole Koropatkin:

[[File:Nicole_Dec2016_small.jpg|200px|right]]Nicole Koropatkin received her PhD in Biochemistry from the University of Wisconsin in 2004. Trained in structural enzymology in the lab of Hazel Holden, her graduate work focused on the enymes involved in O-antigen deoxysugar biosynthesis in Salmonella typhi. After finishing her training, she moved to the lab of Thomas Smith at the Donald Danforth Plant Science Center in St. Louis. She received an NRSA to determine the structural basis for nitrate and bicarbonate discrimination within the ABC transport systems of Synechocystis PCC 6803. After completing this study, she teamed up with Eric Martens from the Jeffrey Gordon lab at Washington University in St. Louis in order to investigate the structures of the novel proteins encoded within Bacteroidetes polysaccharide utilization loci. In 2009 she moved to the University of Michigan Medical School. She is currently an Assistant Professor in the Microbiology and Immunology department. The Koropatkin lab studies the structural biology of glycan capture by a variety of human gut bacteria.

== Selected Citations ==

Koropatkin N, Martens EC, Gordon JI, Smith TJ: Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Biochemistry 48(7): 1532-1542, 2009. [Pubmed ID: 18611383][https://www.ncbi.nlm.nih.gov/pubmed/18611383]

Martens EC, Koropatkin NM, Smith TJ, Gordon JI: Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284(37): 24673-24677, 2009.[Pubmed ID: 19553672] [https://www.ncbi.nlm.nih.gov/pubmed/19553672]

Koropatkin NM, Smith TJ: SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 18(2): 200-215, 2010.

Cameron EA, Kwiatkowski KJ, Lee BH, Hamaker BR, Koropatkin NM, Martens EC: Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis. mBio 5(5): e01441-14, 2014.

Karunatilaka KS, Cameron EA, Martens EC, Koropatkin NM, Biteen JS: Superresolution imaging captures carbohydrate utilization dynamics in human gut symbionts. mBio 5(6): e02172, 2014.

Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM: Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Mol. Microbiol. 95(2): 209-30, 2015.

Foley MH, Cockburn DW, Koropatkin NM: The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Cell Mol Life Sci: 2016.

Tauzin AS, Kwiatkowski KJ, Orlovsky NI, Smith CJ, Creagh AL, Haynes CA, Wawrzak Z, Brumer H, Koropatkin NM: Molecular dissection of xyloglucan recognition in a prominent human gut symbiont. mBio 7(2): e02134-15, 2016.

Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VG, Koropatkin NM, McBride MJ, Pope PB. A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Biotechnol Biofuels. 9:260, 2016.

Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol. Aug 14;428(16):3230-5, 2016

Wefers D, Cavalcante JJV, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie R, Koropatkin N, Cann I. Biochemical assignment of two cryptic proteins in Bacteroides intestinalis as bifunctional esterases and their synergistic activities with cognate xylan degrading enzymes. J Mol Biol. 429 (16):2509-2527, 2017.

== Selected Citations ==
<biblio>
#Koropatkin2009 pmid=18611383
#Martens2009 pmid=19553672
#Koropatkin2010 pmid=20159465
#Cameron2014 pmid=25205092

#Karunatilaka2014 pmid=25389179
#Cockburn2015 pmid=25388295
#Foley2016 pmid=27137179
#Tauzin2016 pmid=27118585
#Larsbrink2016 pmid=27933102
#Cockburn2016 pmid=27393306
#Wefers2017 pmid=28669823

</biblio>


[[Category:Contributors|Koropatkin, Nicole]]

Carbohydrate Binding Module Family 58

2017-09-05T18:27:46Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-05T18:23:06Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-05T18:18:30Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-05T18:16:21Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-05T18:13:06Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-09-05T18:09:34Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-25T00:28:03Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-24T17:09:59Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont Bacteroides thetaiotaomicron. The crystal structure of SusG featuring CBM58 revealed binding to maltoheptaose as well as acarbose. Isothermal titration calorimetry as well as affinity PAGE demonstrates that the CBM58 of SusG binds maltoheptaose, α-cyclodextrin and amylopectin. The CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

''Note: Here is an example of how to insert references in the text, together with the "biblio" section below:'' Please see these references for an essential introduction to the CAZy classification system: ''DaviesSinnott2008 Cantarel2009''. CBMs, in particular, have been extensively reviewed ''Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010''.

== Structural Features ==

The crystal structure of CBM58 from SusG of B. thetaiotaomicron displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, connecting β6 and β7, and β7 and β8. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM (Gilbert/Knox/Boraston.) Like many starch-specific CBMs, the helical α -glucan is cradled by aromatic stacking interactions with two aromatic residues (W287 and W299 in SusG), as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues stacking with the two tryptophans.

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain the, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338 span about 12Å between the A domain and the CBM58 have B-factors and an amino acid sequence imply this domain is held in a fixed position, without inherent flexibility. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum and include similar GH13 enzymes from isolates of Alistipes finegoldii, Alistipes shahii, Bacteroides dorei, Bacteroides eggerthii, and Bacteroides vulgatus. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain.

* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
* '''Type:''' Include here Type A, B, or C and properties
* '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.

== Functionalities ==

''Content in this section should include, in paragraph form, a description of:''

* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.

== Family Firsts ==

; First Identified
: Insert archetype here, possibly including ''very brief'' synopsis.
; First Structural Characterization
: Insert archetype here, possibly including ''very brief'' synopsis.

== References ==

# Cantarel2009 pmid=18838391
# DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
# Boraston2004 pmid=15214846
# Hashimoto2006 pmid=17131061
# Shoseyov2006 pmid=16760304
# Guillen2010 pmid=19908036

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-08-24T17:09:31Z

Nicole Koropatkin:

{{UnderConstruction}}

* [[Author]]: ^^^Nicole Koropatkin^^^
* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM58.html
|}
</div>



== Ligand specificities ==

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont Bacteroides thetaiotaomicron. The crystal structure of SusG featuring CBM58 revealed binding to maltoheptaose as well as acarbose. Isothermal titration calorimetry as well as affinity PAGE demonstrates that the CBM58 of SusG binds maltoheptaose, α-cyclodextrin and amylopectin. The CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

''Note: Here is an example of how to insert references in the text, together with the "biblio" section below:'' Please see these references for an essential introduction to the CAZy classification system: ''DaviesSinnott2008 Cantarel2009''. CBMs, in particular, have been extensively reviewed ''Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010''.

== Structural Features ==
0 0 1 242 1382 University of Michigan 11 3 1621 14.0
The crystal structure of CBM58 from SusG of B. thetaiotaomicron displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, connecting β6 and β7, and β7 and β8. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM (Gilbert/Knox/Boraston.) Like many starch-specific CBMs, the helical α -glucan is cradled by aromatic stacking interactions with two aromatic residues (W287 and W299 in SusG), as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues stacking with the two tryptophans.

0 0 1 138 792 University of Michigan 6 1 929 14.0

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain the, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338 span about 12Å between the A domain and the CBM58 have B-factors and an amino acid sequence imply this domain is held in a fixed position, without inherent flexibility. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum and include similar GH13 enzymes from isolates of Alistipes finegoldii, Alistipes shahii, Bacteroides dorei, Bacteroides eggerthii, and Bacteroides vulgatus. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain.

* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
* '''Type:''' Include here Type A, B, or C and properties
* '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.

== Functionalities ==

''Content in this section should include, in paragraph form, a description of:''

* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
* '''Novel Applications:''' Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.

== Family Firsts ==

; First Identified
: Insert archetype here, possibly including ''very brief'' synopsis.
; First Structural Characterization
: Insert archetype here, possibly including ''very brief'' synopsis.

== References ==

# Cantarel2009 pmid=18838391
# DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
# Boraston2004 pmid=15214846
# Hashimoto2006 pmid=17131061
# Shoseyov2006 pmid=16760304
# Guillen2010 pmid=19908036

[[Category:Carbohydrate Binding Module Families|CBM058]]

Carbohydrate Binding Module Family 58

2017-08-24T16:16:07Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-24T16:15:31Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:52:29Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:52:17Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:50:38Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:49:26Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:47:38Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:46:09Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:45:20Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:43:24Z

Nicole Koropatkin:

Carbohydrate Binding Module Family 58

2017-08-23T22:24:43Z

Nicole Koropatkin:

User:Nicole Koropatkin

2017-08-23T16:03:33Z

Nicole Koropatkin: /* Selected Citations */

[[Image: Nicole_Dec2016_small.jpg|thumb|widthpx| ]]Nicole Koropatkin received her PhD in Biochemistry from the University of Wisconsin in 2004. Trained in structural enzymology in the lab of Hazel Holden, her graduate work focused on the enymes involved in O-antigen deoxysugar biosynthesis in Salmonella typhi. After finishing her training, she moved to the lab of Thomas Smith at the Donald Danforth Plant Science Center in St. Louis. She received an NRSA to determine the structural basis for nitrate and bicarbonate discrimination within the ABC transport systems of Synechocystis PCC 6803. After completing this study, she teamed up with Eric Martens from the Jeffrey Gordon lab at Washington University in St. Louis in order to investigate the structures of the novel proteins encoded within Bacteroidetes polysaccharide utilization loci. In 2009 she moved to the University of Michigan Medical School. She is currently an Assistant Professor in the Microbiology and Immunology department. The Koropatkin lab studies the structural biology of glycan capture by a variety of human gut bacteria.

== Selected Citations ==

Koropatkin N, Martens EC, Gordon JI, Smith TJ: Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Biochemistry 48(7): 1532-1542, 2009. [Pubmed ID: 18611383][https://www.ncbi.nlm.nih.gov/pubmed/18611383]

Martens EC, Koropatkin NM, Smith TJ, Gordon JI: Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284(37): 24673-24677, 2009.[Pubmed ID: 19553672] [https://www.ncbi.nlm.nih.gov/pubmed/19553672]

Koropatkin NM, Smith TJ: SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 18(2): 200-215, 2010.

Cameron EA, Kwiatkowski KJ, Lee BH, Hamaker BR, Koropatkin NM, Martens EC: Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis. mBio 5(5): e01441-14, 2014.

Karunatilaka KS, Cameron EA, Martens EC, Koropatkin NM, Biteen JS: Superresolution imaging captures carbohydrate utilization dynamics in human gut symbionts. mBio 5(6): e02172, 2014.

Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM: Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Mol. Microbiol. 95(2): 209-30, 2015.

Foley MH, Cockburn DW, Koropatkin NM: The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Cell Mol Life Sci: 2016.

Tauzin AS, Kwiatkowski KJ, Orlovsky NI, Smith CJ, Creagh AL, Haynes CA, Wawrzak Z, Brumer H, Koropatkin NM: Molecular dissection of xyloglucan recognition in a prominent human gut symbiont. mBio 7(2): e02134-15, 2016.

Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VG, Koropatkin NM, McBride MJ, Pope PB. A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Biotechnol Biofuels. 9:260, 2016.

Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol. Aug 14;428(16):3230-5, 2016

Wefers D, Cavalcante JJV, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie R, Koropatkin N, Cann I. Biochemical assignment of two cryptic proteins in Bacteroides intestinalis as bifunctional esterases and their synergistic activities with cognate xylan degrading enzymes. J Mol Biol. 429 (16):2509-2527, 2017.

User:Nicole Koropatkin

2017-08-23T16:02:00Z

Nicole Koropatkin: /* Selected Citations */

[[Image: Nicole_Dec2016_small.jpg|thumb|widthpx| ]]Nicole Koropatkin received her PhD in Biochemistry from the University of Wisconsin in 2004. Trained in structural enzymology in the lab of Hazel Holden, her graduate work focused on the enymes involved in O-antigen deoxysugar biosynthesis in Salmonella typhi. After finishing her training, she moved to the lab of Thomas Smith at the Donald Danforth Plant Science Center in St. Louis. She received an NRSA to determine the structural basis for nitrate and bicarbonate discrimination within the ABC transport systems of Synechocystis PCC 6803. After completing this study, she teamed up with Eric Martens from the Jeffrey Gordon lab at Washington University in St. Louis in order to investigate the structures of the novel proteins encoded within Bacteroidetes polysaccharide utilization loci. In 2009 she moved to the University of Michigan Medical School. She is currently an Assistant Professor in the Microbiology and Immunology department. The Koropatkin lab studies the structural biology of glycan capture by a variety of human gut bacteria.

== Selected Citations ==

Koropatkin N, Martens EC, Gordon JI, Smith TJ: Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Biochemistry 48(7): 1532-1542, 2009. [Pubmed ID: 18611383][https://www.ncbi.nlm.nih.gov/pubmed/18611383]

Martens EC, Koropatkin NM, Smith TJ, Gordon JI: Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284(37): 24673-24677, 2009.

Koropatkin NM, Smith TJ: SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 18(2): 200-215, 2010.

Cameron EA, Kwiatkowski KJ, Lee BH, Hamaker BR, Koropatkin NM, Martens EC: Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis. mBio 5(5): e01441-14, 2014.

Karunatilaka KS, Cameron EA, Martens EC, Koropatkin NM, Biteen JS: Superresolution imaging captures carbohydrate utilization dynamics in human gut symbionts. mBio 5(6): e02172, 2014.

Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM: Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Mol. Microbiol. 95(2): 209-30, 2015.

Foley MH, Cockburn DW, Koropatkin NM: The Sus operon: a model system for starch uptake by the human gut Bacteroidetes. Cell Mol Life Sci: 2016.

Tauzin AS, Kwiatkowski KJ, Orlovsky NI, Smith CJ, Creagh AL, Haynes CA, Wawrzak Z, Brumer H, Koropatkin NM: Molecular dissection of xyloglucan recognition in a prominent human gut symbiont. mBio 7(2): e02134-15, 2016.

Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VG, Koropatkin NM, McBride MJ, Pope PB. A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Biotechnol Biofuels. 9:260, 2016.

Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol. Aug 14;428(16):3230-5, 2016

Wefers D, Cavalcante JJV, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie R, Koropatkin N, Cann I. Biochemical assignment of two cryptic proteins in Bacteroides intestinalis as bifunctional esterases and their synergistic activities with cognate xylan degrading enzymes. J Mol Biol. 429 (16):2509-2527, 2017.