Carbohydrate Binding Module Family 58 - Revision history

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

2021-12-18T21:15:33Z

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

Elizabeth Ficko-Blean: /* Structural Features */

2018-03-06T16:15:37Z

Structural Features

Harry Brumer: added PDB link

2017-09-13T03:53:44Z

added PDB link

Harry Brumer: fixed line spacing at top of page

2017-09-10T21:16:46Z

fixed line spacing at top of page

Harry Brumer: Moved Fig. 1 to right

2017-09-10T21:15:49Z

Moved Fig. 1 to right

Nicole Koropatkin at 20:05, 10 September 2017

2017-09-10T20:05:48Z

Nicole Koropatkin at 20:03, 10 September 2017

2017-09-10T20:03:34Z

Nicole Koropatkin at 20:02, 10 September 2017

2017-09-10T20:02:13Z

Nicole Koropatkin at 20:01, 10 September 2017

2017-09-10T20:01:26Z

Harry Brumer: fixed broken Grondin ref

2017-09-08T23:38:37Z

fixed broken Grondin ref

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Nicole Koropatkin^^^
+* [[Author]]: [[User:Nicole Koropatkin|Nicole Koropatkin]]
-* [[Responsible Curator]]: ^^^Nicole Koropatkin^^^
+* [[Responsible Curator]]: [[User:Nicole Koropatkin|Nicole Koropatkin]]
 ----

@@ Line 21: / Line 21: @@
 == 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>.
+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 [[Carbohydrate-binding_modules#Types|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 ==

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-[[File:SusG_Cazy.png|thumb|400px|right|'''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. ]]
+[[File:SusG_Cazy.png|thumb|400px|right|'''Figure 1: ''B. thetaiotaomicron'' SusG.''' Cartoon representation of the crystal structure of the catalytically inactive SusG D498N mutant complexed with maltoheptaose ([{{PDBlink}}3k8l 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.

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
 * [[Author]]: ^^^Nicole Koropatkin^^^
 * [[Responsible Curator]]: ^^^Nicole Koropatkin^^^
 ----
 <!-- The data in the table below should be updated by the Author/Curator according to current information on the family -->
 <div style="float: right">
@@ Line 17: / Line 14: @@
 |}
 </div>
 <!-- This is the end of the table -->

@@ Line 21: / Line 21: @@
 == 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. ]]
+[[File:SusG_Cazy.png|thumb|400px|right|'''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.

@@ Line 26: / Line 26: @@
 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 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 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 1). The majority of these CBM58-containing proteins are expressed within canonical polysaccharide utilization loci <cite>Foley2016 Grondin 2017</cite> 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 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 1). 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 ==