CAZypedia - User contributions [en-ca]

Carbohydrate Binding Module Family 60

2018-02-06T07:51:13Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprises around 120 amino acids. The CBM60s from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. ITC experiments were performed using a large set of polysaccharides and oligosaccharides <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively <cite>Montanier2010</cite>. Cell labelling of plant cell wall sections indicated that xylan is the biologically relevant ligand for the two characterized CBM60s <cite>Montanier2010</cite>. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein as demonstrated by gel filtration only with ''Cj''CBM60A <cite>Montanier2010</cite>. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60A (compared to ''v''CBM60), which contains cysteines, mediates dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was enthalpy-driven and highlighted a single carbohydrate binding site per CBM <cite>Montanier2010</cite>. Each protein molecule covered 4-6 sugars at saturation, displaying a similar affinity for long polysaccharides, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA <cite>Montanier2010</cite>. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60 <cite>Montanier2010</cite>.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanases, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site. Cell wall labelling experiments were carried out using intact cell walls of tobacco stem sections by immunohistochemistry <cite>Montanier2010</cite>.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-02-06T07:48:51Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprises around 120 amino acids. The CBM60s from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. ITC experiments were performed using a large set of polysaccharides and oligosaccharides <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively <cite>Montanier2010</cite>. Cell labelling of plant cell wall sections indicated that xylan is the biologically relevant ligand for the two characterized CBM60s <cite>Montanier2010</cite>. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein as demonstrated by gel filtration only with ''Cj''CBM60A <cite>Montanier2010</cite>. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediates dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was enthalpy-driven and highlighted a single carbohydrate binding site per CBM <cite>Montanier2010</cite>. Each protein molecule covered 4-6 sugars at saturation, displaying a similar affinity for long polysaccharides, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA <cite>Montanier2010</cite>. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60 <cite>Montanier2010</cite>.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanases, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site. Cell wall labelling experiments were carried out using intact cell walls of tobacco stem sections by immunohistochemistry <cite>Montanier2010</cite>.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-02-06T07:45:03Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprises around 120 amino acids. The CBM60s from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. ITC experiments were perforemd using a large set of polysaccharides and oligosaccharides <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively <cite>Montanier2010</cite>. Cell labelling of plant cell wall sections indicated that xylan is the biologically relevant ligand for the two characterized CBM60s <cite>Montanier2010</cite>. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein as demonstrated by gel filtration only with ''Cj''CBM60A <cite>Montanier2010</cite>. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediates dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was enthalpy-driven and highlighted a single carbohydrate binding site per CBM <cite>Montanier2010</cite>. Each protein molecule covered 4-6 sugars at saturation, displaying a similar affinity for long polysaccharides, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA <cite>Montanier2010</cite>. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60 <cite>Montanier2010</cite>.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanases, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site. Cell wall labelling experiments were carried out using intact cell walls of tobacco stem sections by immunohistochemistry <cite>Montanier2010</cite>.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-02-06T07:44:04Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprises around 120 amino acids. The CBM60s from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. ITC experiments were perforemd using a large set of polysaccharides and oligosaccharides <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively <cite>Montanier2010</cite>. Cell labelling of plant cell wall sections indicated that xylan is the biologically relevant ligand for the two characterized CBM60s <cite>Montanier2010</cite>. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein as demonstrated by gel filtration only with ''Cj''CBM60A <cite>Montanier2010</cite>. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediates dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was enthalpy-driven and highlighted a single carbohydrate binding site per CBM <cite>Montanier2010</cite>. Each protein molecule covered 4-6 sugars at saturation, displaying a similar affinity for long polysaccharides, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA <cite>Montanier2010</cite>. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60 <cite>Montanier2010</cite>.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanases, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site. Cell wall labelling experiments were carried out using intact cell walls of tobacco stem sections using immunohistochemistry <cite>Montanier2010</cite>.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-02-06T07:35:57Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprises around 120 amino acids. The CBM60s from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. ITC experiments were perforemd using a large set of polysaccharides and oligosaccharides <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively <cite>Montanier2010</cite>. Cell labelling of plant cell wall sections indicated that xylan is the biologically relevant ligand for the two characterized CBM60s <cite>Montanier2010</cite>. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein as demonstrated by gel filtration <cite>Montanier2010</cite>. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediates dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was enthalpy-driven and highlighted a single carbohydrate binding site per CBM <cite>Montanier2010</cite>. Each protein molecule covered 4-6 sugars at saturation, displaying a similar affinity for long polysaccharides, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA <cite>Montanier2010</cite>. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60 <cite>Montanier2010</cite>.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanases, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-02-06T07:32:07Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprises around 120 amino acids. The CBM60s from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. ITC experiments were perforemd using a large set of polysaccharides and oligosaccharides <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively <cite>Montanier2010</cite>. Cell labelling of plant cell wall sections indicated that xylan is the biologically relevant ligand for the two characterized CBM60s <cite>Montanier2010</cite>. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein as demonstrated by gel filtration <cite>Montanier2010</cite>. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediates dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was enthalpy-driven and highlighted a single carbohydrate binding site per CBM <cite>Montanier2010</cite>. by enthalpy with each protein molecule covering 4-6 sugars at saturation, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA <cite>Montanier2010</cite>. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60 <cite>Montanier2010</cite>.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanases, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-02-06T07:06:28Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprises around 120 amino acids. The CBM60s from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively <cite>Montanier2010</cite>. Cell labelling of plant cell wall sections indicated that xylan is the biologically relevant ligand for the two characterized CBM60s <cite>Montanier2010</cite>. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein as demonstrated by gel filtration <cite>Montanier2010</cite>. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediates dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was driven by enthalpy with each protein molecule covering 4-6 sugars at saturation, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA <cite>Montanier2010</cite>. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60 <cite>Montanier2010</cite>.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanases, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-01-22T16:01:35Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprise around 120 amino acids. The CBM60 from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively. Cell labelling of plant cell wall sections indicated that xylan was the biologically relevant ligand for the two characterized CBM60s. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein demonstrated by gel filtration. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediate dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was driven by enthalpy with each protein molecule covering 4-6 sugars at saturation, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanses, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-01-22T10:14:35Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprise around 120 amino acids. The CBM60 from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively. Cell labelling of plant cell wall sections indicated that xylan was the biologically relevant ligand for the two characterized CBM60s. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein demonstrated by gel filtration. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediate dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was driven by enthalpy with each protein molecule covering 4-6 sugars at saturation, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XHH PDB ID 2XHH]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanses, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-01-22T10:13:04Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprise around 120 amino acids. The CBM60 from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively. Cell labelling of plant cell wall sections indicated that xylan was the biologically relevant ligand for the two characterized CBM60s. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein demonstrated by gel filtration. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediate dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was driven by enthalpy with each protein molecule covering 4-6 sugars at saturation, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFH PDB ID 2XFH]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanses, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-01-22T10:11:16Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprise around 120 amino acids. The CBM60 from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively. Cell labelling of plant cell wall sections indicated that xylan was the biologically relevant ligand for the two characterized CBM60s. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein demonstrated by gel filtration. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediate dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was driven by enthalpy with each protein molecule covering 4-6 sugars at saturation, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes with ''v''CBM60, galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanses, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-01-22T10:08:09Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprise around 120 amino acids. The CBM60 from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively. Cell labelling of plant cell wall sections indicated that xylan was the biologically relevant ligand for the two characterized CBM60s. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein demonstrated by gel filtration. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediate dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was driven by enthalpy with each protein molecule covering 4-6 sugars at saturation, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes of ''v''CBM60 galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding mannose-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanses, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 60

2018-01-22T10:05:03Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM60.html
|}
</div>


== Ligand specificities ==
CBM60 is a bacterial family that comprise around 120 amino acids. The CBM60 from the ''Cellvibrio japonicus'' GH11 xylanase ''Cj''Xyn11A (''Cj''CBM60A) and a second GH11 xylanase (''v''CBM60), derived from an uncultured bacterium, were shown to display similar broad ligand specificities binding to galactan, xylans, and β-glucans <cite>Montanier2010</cite>. Affinities (''K''<sub>D</sub>) for ligands were in the high and very low µM range for ''Cj''CBM60A and ''v''CBM60, respectively. Cell labelling of plant cell wall sections indicated that xylan was the biologically relevant ligand for the two characterized CBM60s. ''v''CBM60 bound to oligosaccharides with a degree of polymerization (DP) of 2 or 3 with affinities similar to the cognate polysaccharide. Binding of ''Cj''CBM60A to xylooligosaccharides that extended outside the predicted ligand binding site were 20-30-fold lower than for the xylans. This increased affinity for the polysaccharide compared to oligosaccharides is an example of avidity effects through dimerization of the protein demonstrated by gel filtration. It was proposed that the 10 residue C-terminal extension of ''Cj''CBM60 (compared to ''v''CBM60), which contains cysteines, mediate dimerization through the formation of inter-chain disulphide bonds <cite>Montanier2010</cite>. The affinity of the CBM60s for their ligands was driven by enthalpy with each protein molecule covering 4-6 sugars at saturation, indicating an endo-mode of binding. This endo-mode of binding to soluble polysaccharide chains indicates that ''v''CBM60 and ''Cj''CBM60 are type B CBMs.

== Structural Features ==

[[File:CBM60fold.png|thumb|300px|right|'''Figure 1.''' The fold of ''v''CBM60 in complex with galactobiose ([{{PDBlink}}2XFE PDB ID 2XFE]), highlighting the location of the ligand binding site formed by three loops connecting the two β-sheets.]]

[[File:galactobiosecomplex.png|thumb|300px|right|'''Figure 2.''' The structure of ''v''CBM60 in complex with galactobiose showing the role played by two aspartates in direct ligand recognition and via a calcium. Interactions are exclusively with O2 and O3 of the non-reducing galactose illustrating the broad specificity of the CBM for sugars containing an equatorial O2 and O3. The second binding site interacts with the ligand through hydrophobic interactions provided by a tryptophan.]]

The crystal structure of ''v''CBM60 in complex with cellotriose and galactobiose revealed a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands (Figure 1 <cite>Montanier2010</cite>). The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala75- Glu76- Asn77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep) that is stabilized by a disulphide bond (Figure 1; [{{PDBlink}}2XFE PDB ID 2XFE]). In complexes of vCBM60 galactobiose (Figure 2; [{{PDBlink}}2XFE PDB ID 2XFE]) and cellotriose ([{{PDBlink}}2XFD PDB ID 2XFD]) are located in the cleft, which thus comprises the ligand binding site. Unusually for an endo-acting CBM the ligand binding cleft contains only two sugar sites. The reducing end sugar makes hydrophobic contacts with Trp85. The non-reducing end sugar also makes non-polar contacts with Trp85 but sugar binding is dominated by the side chains of two aspartates. The carboxylates of these residues hydrogen bonds with O2 and O3 of the sugar, and interact with a calcium. This divalent metal ion also makes polar interactions with O2 and O3 of the sugar (Figure 2). The essential role played by the two aspartates, Trp85 and calcium was confirmed by mutagenesis and metal chelation with EDTA. The specificity for equatorial O2 and O3, with no interactions with O4 and O6, explain why the CBM can bind to a range of hexose and pentose pyranose sugars, while excluding manno-configured ligands where O2 is axial. Based on the conservation of the ligand binding residues in other family 60 CBMs, it was predicted that ligand recognition is similarly conserved in CBM60.
== Functionalities ==
''Cj''CBM60 is derived from an enzyme containing a GH11 xylanase (Asn26 to Glu227), a CBM60 (Ile256-Cys370), a CE4 esterase (Gly398-Pro586) and a C-terminal CBM10 (Asn614-Asn661) <cite>Millward-Sadler1995</cite>. ''v''CBM60 is located in a GH11 xylanase, but no further information regarding additional modules is available. CBM60s are found in a number of GH11 xylanases, some of which contain esterase catalytic modules and additional CBMs. A cohort of these CBMs are also found in GH53 enzymes that are predicted to be endo-β1,4-galactanses, consistent with their recognition of galactan in addition to xylan. Some of the CBM60s contains the C-terminal extension evident in ''Cj''CBM60, and it was proposed that these modules dimerize leading to increased affinity through avidity effects <cite>Montanier2010</cite>. CBM60 shares with family 36 CBMs a conserved metal ion playing a dominant role in binding carbohydrates with an equatorial O2 and O3 <cite>Jamal2004</cite>. This is consistent with the similar ligand specificities displayed by the two families. Sequence and structural analyses revealed that the family 60 CBM arose through the circular permutation of CBM36 <cite>Jamal2004</cite>. The reorganization of the β-sandwich fold did not disrupt the topology of the binding site.
== Family Firsts ==
;First Identified
The first CBM60s to be characterized were ''Cj''CBM60A from GH11 ''C. japonicus'' xylanase ''Cj''Xyn11A (originally defined as XYLE) and ''v''CBM60 obtained from an environmental library of GH11 xylanases <cite>Montanier2010</cite>.
;First Structural Characterization
The first crystal structure of this family is ''v''CBM60 <cite>Montanier2010</cite>.
== References ==
<biblio>
#Montanier2010 pmid=20659893

#Millward-Sadler1995 pmid=7492333

#Jamal2004 pmid=15242594
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM060]]

Carbohydrate Binding Module Family 62

2015-01-14T07:34:19Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects <cite>Boraston2002,Vijayan1999</cite>.
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Montanier2011 pmid=21454512
#Correia2011 pmid=21378160
#Boraston2002 pmid=11849546
#Vijayan1999 pmid=10607664
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-14T07:32:55Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects <cite>Boraston2002,Vijayan1999</cite>.
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Montanier2011 pmid=21454512
#Correia2011 pmid=21378160
#Vijayan1999 pmid=10607664
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-14T07:32:26Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A <cite>Correia2011</cite>. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects <cite>Vijayan1999</cite>.
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Montanier2011 pmid=21454512
#Correia2011 pmid=21378160
#Vijayan1999 pmid=10607664
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-14T07:24:46Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Montanier2011 pmid=21454512
#Correia2011 pmid=21378160
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-14T07:21:27Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase <cite>Correia2011</cite>. It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Montanier2011 pmid=21454512
#Correia2011 pmid=21378160
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-14T07:15:29Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Montanier2011 pmid=21454512
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-14T07:13:52Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Montanier2011 pmid=18838391
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-14T07:12:59Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Montanier2011
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-14T07:08:29Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose <cite>Montanier2011</cite>. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T11:39:01Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, ''Ct''CBM62 recognises terminal sugars.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T11:37:59Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars.

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T11:37:11Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the CtCBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T11:36:42Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

''Ct''CBM62 from the ''Clostridium thermocellum'' multi-modular xylanase CtXyl5A.

;First Structural Characterization

The first available crystal structure and the first complex structure of a CBM62 is from ''Ct''CBM62.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T11:30:55Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified

CtCBM62 from the Clostridium thermocellum multidomaine xylanase CtXyl5A.

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

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T11:30:15Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A (ref). It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''Xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified
CtCBM62 from the Clostridium thermocellum multidomaine xylanase CtXyl5A.
:Insert archetype here, possibly including ''very brief'' synopsis.
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T10:23:23Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the ''Ct''CBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 6<sup>1</sup>-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of ''Ct''CBM62 revealed that the interactions between the protein and the α-<sub>L</sub> pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of ''Ct''CBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of ''Ct''CBM62 corresponds to residues 739-878 of full length ''Ct''Xyl5A. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

''Ct''CBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. ''Ct''CBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to ''Ct''CBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to ''Ct''CBM62 in a similar way to galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
''Ct''CBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain ''Ct''Xyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for ''Ct''xyl5A is an arabinoxylan that also contains D-galactose side chains recognized by ''Ct''CBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by ''Ct''CBM62 and bringing the catalytic module of ''Ct''Xyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, ''Ct''CBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified
:Insert archetype here, possibly including ''very brief'' synopsis.
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T10:16:25Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the CtCBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 61-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of CtCBM62 revealed that the interactions between the protein and the α-L pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of CtCBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of CtCBM62 corresponds to residues 739-878 of full length CtXyl5A. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

CtCBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. CtCBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to CtCBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to CtCBM62 in a similar way to Galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
CtCBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain CtXyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for Ctxyl5A is an arabinoxylan that also contains D-galactose side chains recognized by CtCBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by CtCBM62 and bringing the catalytic module of CtXyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, CtCBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified
:Insert archetype here, possibly including ''very brief'' synopsis.
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T10:16:08Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the CtCBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 61-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of CtCBM62 revealed that the interactions between the protein and the α-L pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of CtCBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of CtCBM62 corresponds to residues 739-878 of full length CtXyl5A. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

CtCBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. CtCBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to CtCBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to CtCBM62 in a similar way to Galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== Functionalities ==
CtCBM62 targets polysaccharides containing terminal D-galactose or L-arabinopyranose residues, whereas the appended catalytic domain CtXyl5A from family GH5 is an arabinoxylan-specific xylanase (Correia, A. S., Mazumder, K., Bras, J. L., Firbank, S. J., Zhu, Y., Lewis, R. J.,York, W. S., Fontes, C. M., and Gilbert, H. J. (2011) J. Biol. Chem. 286). It is possible that the primary substrate for Ctxyl5A is an arabinoxylan that also contains D-galactose side chains recognized by CtCBM62 or that arabinoxylans are in close association with polysaccharides displaying D-galactose or L-arabinofuranose targeted by CtCBM62 and bringing the catalytic module of CtXyl5A into close proximity whith its substrate.

It has been demonstrated that in the presence of calcium, CtCBM62 binds ≈ 200-fold more tightly to the galactosyl side-chains of the decorated ligands galactomannan and ≈ 100-fold xyloglucan, than to galactose. Such binding is associated with the formation of an insoluble polysaccharides lattice, which is a classic features of avidity effects (ref).
== Family Firsts ==
;First Identified
:Insert archetype here, possibly including ''very brief'' synopsis.
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T10:14:38Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the CtCBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 61-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of CtCBM62 revealed that the interactions between the protein and the α-L pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of CtCBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==

The final structure of CtCBM62 corresponds to residues 739-878 of full length CtXyl5A. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

CtCBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. CtCBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to CtCBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to CtCBM62 in a similar way to Galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== 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 ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T10:14:13Z

Cedric Montanier:

{{UnderConstruction}}
* [[Author]]: ^^^Cedric Montanier^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM62.html
|}
</div>


== Ligand specificities ==

<nowiki>The only known crystallographic structure of a carbohydrate-binding module of family 62 is the CtCBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 61-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of CtCBM62 revealed that the interactions between the protein and the α-L pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of CtCBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose.

Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars. </nowiki>

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

''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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.

== Structural Features ==
''Content in this section should include, in paragraph form, a description of:''
* '''Fold:'''

The final structure of CtCBM62 corresponds to residues 739-878 of full length CtXyl5A. It presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 25, Asp 30 and Ala 130, the Oε2 of Asp 28 and Glu 131, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 33.

CtCBM62 displays a shallow surface groove, containing Trp 44 that runs along the whole of the concave face of the jelly-roll, which could be, by analogy with other CBMs, a ligand-binding site. However, a second tryptophan, Trp 16, is present in the loop area on the top of the β-jelly-roll where a pocket ≈ 7.5 Å wide and ≈ 5 Å deep is located, which is the ligand-binding site. CtCBM62 is thus a type C CBM.

Galactopyranose moiety of both xyloglucan oligosaccharide and GM3 is bound to CtCBM62 through hydrogen bonds with the side-chains of Asp 36, Arg 65, Tyr 68 and Arg 71 in a shallow binding pocket, while indole side-chain of Trp 16 makes a hydrophobic interaction with the sugar ring. The OH of Tyr 68 hydrogen bonds to the O2 of Gal, while an NH2 of Arg 65 also interacts with the C2 hydroxyl of the hexose sugar. O3 of the sugar ring is hydrogen bonded to the protein by both NH2 of Arg 65 in addition to an O of Asp 36. The C4 hydroxyl is tetra coordinated by a NH2 of Arg 65, both side-chain oxygens of Asp 36 and an NH2 of Arg 71, while the second amine group of Arg 71 hydrogen bonds to the oxygen ring of Gal. The xylose moiety of xyloglucan oligosaccharide does not interact with CtCBM62, but O of the β-1,2 linkage binds to the OH of Tyr 68 and an NH2 of Arg 71. The arabinopyranose is bound to CtCBM62 in a similar way to Galactose, except that the hydroxyl in C2 is hydrogen bonded only to the OH of Tyr 68.

== 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 ==
<biblio>
#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM062]]

Carbohydrate Binding Module Family 62

2015-01-08T10:08:29Z

Cedric Montanier:

Carbohydrate Binding Module Family 62

2014-12-24T12:48:10Z

Cedric Montanier:

Carbohydrate Binding Module Family 62

2014-12-24T12:47:06Z

Cedric Montanier:

Carbohydrate Binding Module Family 62

2014-12-24T12:44:14Z

Cedric Montanier:

Carbohydrate Binding Module Family 62

2014-12-24T12:42:39Z

Cedric Montanier:

Carbohydrate Binding Module Family 60

2014-12-24T12:40:11Z

Cedric Montanier:

Carbohydrate Binding Module Family 60

2014-12-24T12:24:29Z

Cedric Montanier:

User:Cedric Montanier

2014-02-18T16:20:06Z

Cedric Montanier:

[[Image:CM.jpg|thumb|widthpx| ]]This is the user page of '''Cédric Montanier'''. My first contact with the carbohydrate-active enzymes was motivated by the functional significance of peptide motifs conserved in large multigene glycosyltransferase families, in particular the GT8 family. This work was done with Christelle Breton from CERMAV (Grenoble, France) and Catherine Letondal from Institut Pasteur (Paris, France). In 2004, I then moved further North to Newcastle-upon-Tyne in England for a PhD under the supervision of Harry Gilbert. The work focused on the mechanism and functional importance of protein carbohydrate recognition, more specifically with the families CBM35, 60 and 62 and the family CE2, using a combination of X-ray crystallography, enzyme kinetics and isothermal titration calorimetry. I then followed the sun to the South of France, in Toulouse, where I joined the Enzyme Molecular Engineering and Catalysis group headed by Magali Remaud-Siméon, for two post-docs. The topic of the first one was to design by rational engineering a lipase from Candida antarctica in order to synthetized ecofriendly ester and amide based polymers. During my second post-doc, I moved back to the carbohydrate-active enzymes, as I developed by molecular engineering a xylane glycoside hydrolase into a transglycosidase in order to synthetize tailored xylooligosaccharides directly from biomass-isolated pentose fraction. In 2012, I obtained a permanent research scientist position at INRA (French National Institute for Agricultural Research) in the group of Michael O'Donohue, based in Toulouse. My main interest is to understand the synergism between GHs leading to the deconstruction of plant cell wall and the contribution of the CBMs occurring during this complex process. My background in enzyme engineering leads me to develop an artificial cellulosome to understand the synergism activity of several GHs, on insoluble substrates and intact plant cell wall. I am also interested in new approach to visualize and quantify the result of a deconstruction process, for instance using X-ray computed micro-tomography.

http://www.lisbp.insa-toulouse.fr

User:Cedric Montanier

2014-02-18T16:19:19Z

Cedric Montanier:

[[Image:CM.jpg|thumb|widthpx| ]]This is the user page of '''Cédric Montanier'''. My first contact with the carbohydrate-active enzymes was motivated by the functional significance of peptide motifs conserved in large multigene glycosyltransferase families, in particular the GT8 family. This work was done with Christelle Breton from CERMAV (Grenoble, France) and Catherine Letondal from Institut Pasteur (Paris, France). In 2004, I then moved further North to Newcastle-upon-Tyne in England for a PhD under the supervision of Harry Gilbert. The work focused on the mechanism and functional importance of protein carbohydrate recognition, more specifically with the families CBM35, 60 and 62 and the family CE2, using a combination of X-ray crystallography, enzyme kinetics and isothermal titration calorimetry. I then followed the sun to the South of France, in Toulouse, where I joined the Enzyme Molecular Engineering and Catalysis group headed by Magali Remaud-Siméon, for two post-docs. The topic of the first one was to design by rational engineering a lipase from Candida antarctica in order to synthetized ecofriendly ester and amide based polymers. During my second post-doc, I moved back to the carbohydrate-active enzymes, as I developed by molecular engineering a xylane glycoside hydrolase into a transglycosidase in order to synthetize tailored xylooligosaccharides directly from biomass-isolated pentose fraction. In 2012, I obtained a permanent research scientist position at INRA (French National Institute for Agricultural Research)in the group of Michael O'Donohue, based in Toulouse. My main interest is to understand the synergism between GHs leading to the deconstruction of plant cell wall and the contribution of the CBMs occurring during this complex process. My background in enzyme engineering leads me to develop an artificial cellulosome to understand the synergism activity of several GHs, on insoluble substrates and intact plant cell wall. I am also interested in new approach to visualize and quantify the result of a deconstruction process, for instance using X-ray computed micro-tomography.

http://www.lisbp.insa-toulouse.fr

User:Cedric Montanier

2014-02-18T16:17:02Z

Cedric Montanier:

[[Image:CM.jpg|thumb|widthpx| ]]This is the user page of '''Cédric Montanier'''. My first contact with the carbohydrate-active enzymes was motivated by the functional significance of peptide motifs conserved in large multigene glycosyltransferase families, in particular the GT8 family. This work was done with Christelle Breton from CERMAV (Grenoble, France) and Catherine Letondal from Institut Pasteur (Paris, France). In 2004, I then moved further North to Newcastle-upon-Tyne in England for a PhD under the supervision of Harry Gilbert. The work focused on the mechanism and functional importance of protein carbohydrate recognition, more specifically with the families CBM35, 60 and 62 and the family CE2, using a combination of X-ray crystallography, enzyme kinetics and isothermal titration calorimetry. I then followed the sun to the South of France, in Toulouse, where I joined the Enzyme Molecular Engineering and Catalysis group headed by Magali Remaud-Siméon, for two post-docs. The topic of the first one was to design by rational engineering a lipase from Candida antarctica in order to synthetized ecofriendly ester and amide based polymers. During my second post-doc, I moved back to the carbohydrate-active enzymes, as I developed by molecular engineering a xylane glycoside hydrolase into a transglycosidase in order to synthetize tailored xylooligosaccharides directly from biomass-isolated pentose fraction. In 2012, I obtained a permanent research scientist position at INRA (French National Institute for Agricultural Research), based in Toulouse. My main interest is to understand the synergism between GHs leading to the deconstruction of plant cell wall and the contribution of the CBMs occurring during this complex process. My background in enzyme engineering leads me to develop an artificial cellulosome to understand the synergism activity of several GHs, on insoluble substrates and intact plant cell wall. I am also interested in new approach to visualize and quantify the result of a deconstruction process, for instance using X-ray computed micro-tomography.

http://www.lisbp.insa-toulouse.fr

User:Cedric Montanier

2014-02-18T16:16:31Z

Cedric Montanier:

[[Image:CM.jpg|thumb|widthpx| ]]This is the user page of Cédric Montanier. My first contact with the carbohydrate-active enzymes was motivated by the functional significance of peptide motifs conserved in large multigene glycosyltransferase families, in particular the GT8 family. This work was done with Christelle Breton from CERMAV (Grenoble, France) and Catherine Letondal from Institut Pasteur (Paris, France). In 2004, I then moved further North to Newcastle-upon-Tyne in England for a PhD under the supervision of Harry Gilbert. The work focused on the mechanism and functional importance of protein carbohydrate recognition, more specifically with the families CBM35, 60 and 62 and the family CE2, using a combination of X-ray crystallography, enzyme kinetics and isothermal titration calorimetry. I then followed the sun to the South of France, in Toulouse, where I joined the Enzyme Molecular Engineering and Catalysis group headed by Magali Remaud-Siméon, for two post-docs. The topic of the first one was to design by rational engineering a lipase from Candida antarctica in order to synthetized ecofriendly ester and amide based polymers. During my second post-doc, I moved back to the carbohydrate-active enzymes, as I developed by molecular engineering a xylane glycoside hydrolase into a transglycosidase in order to synthetize tailored xylooligosaccharides directly from biomass-isolated pentose fraction. In 2012, I obtained a permanent research scientist position at INRA (French National Institute for Agricultural Research), based in Toulouse. My main interest is to understand the synergism between GHs leading to the deconstruction of plant cell wall and the contribution of the CBMs occurring during this complex process. My background in enzyme engineering leads me to develop an artificial cellulosome to understand the synergism activity of several GHs, on insoluble substrates and intact plant cell wall. I am also interested in new approach to visualize and quantify the result of a deconstruction process, for instance using X-ray computed micro-tomography.

http://www.lisbp.insa-toulouse.fr

User:Cedric Montanier

2014-02-18T16:11:16Z

Cedric Montanier:

This is the user page of Cédric Montanier. My first contact with the carbohydrate-active enzymes was motivated by the functional significance of peptide motifs conserved in large multigene glycosyltransferase families, in particular the GT8 family. This work was done with Christelle Breton from CERMAV (Grenoble, France) and Catherine Letondal from Institut Pasteur (Paris, France). In 2004, I then moved further North to Newcastle-upon-Tyne in England for a PhD under the supervision of Harry Gilbert. The work focused on the mechanism and functional importance of protein carbohydrate recognition, more specifically with the families CBM35, 60 and 62 and the family CE2, using a combination of X-ray crystallography, enzyme kinetics and isothermal titration calorimetry. I then followed the sun to the South of France, in Toulouse, where I joined the Enzyme Molecular Engineering and Catalysis group headed by Magali Remaud-Siméon, for two post-docs. The topic of the first one was to design by rational engineering a lipase from Candida antarctica in order to synthetized ecofriendly ester and amide based polymers. During my second post-doc, I moved back to the carbohydrate-active enzymes, as I developed by molecular engineering a xylane glycoside hydrolase into a transglycosidase in order to synthetize tailored xylooligosaccharides directly from biomass-isolated pentose fraction. In 2012, I obtained a permanent research scientist position at INRA (French National Institute for Agricultural Research), based in Toulouse. My main interest is to understand the synergism between GHs leading to the deconstruction of plant cell wall and the contribution of the CBMs occurring during this complex process. My background in enzyme engineering leads me to develop an artificial cellulosome to understand the synergism activity of several GHs, on insoluble substrates and intact plant cell wall. I am also interested in new approach to visualize and quantify the result of a deconstruction process, for instance using X-ray computed micro-tomography.

http://www.lisbp.insa-toulouse.fr

File:CM.jpg

2014-02-18T16:10:03Z

Cedric Montanier:

User:Cedric Montanier

2014-02-18T15:57:00Z

Cedric Montanier: Created page with "This is the user page of Cédric Montanier. My first contact with the carbohydrate-active enzymes was motivated by the functional significance of peptide motifs conserved in l..."