CAZypedia - User contributions [en-ca]

Carbohydrate Binding Module Family 67

2018-11-16T01:19:14Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a [[GH78]] α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but it did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly, the D179A and N180A mutants of SaCBM67, in which removed hydrogen bonds with calcium, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was observed <cite>Fujimoto2013</cite>.

== Structural Features ==
SaCBM67 is a ʟ-rhamnose binding module. The exo binding manner with shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, A, and C)<cite>Fujimoto2013</cite>. Domain D designated SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.

[[File:SaCBM67_3.png|thumb|300px|right|'''Figure 1.''' The structure of ʟ-rhamnose binding pocket of SaCBM67 [{{PDBlink}}3w5n 3W5N].]]

== Functionalities ==
Although SaCBM67 shows 2 times higher affinity for ʟ-rhamnose than ʟ-mannose<cite>Fujimoto2013</cite>. It binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually D179A and N180A mutant enzymes losted binding ability to ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide, these mutations did not influence activity against aryl-rhamnosides <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial [[GH78]] α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree<cite>Fujimoto2013</cite>. Although the calcium binding site is conserved in CBM67 members, these CBM67 members might show different sugar specificities because the ʟ-rhamnose binding residues in SaCBM67 are not retained in all the subfamilies. For example, the lectin from ''Pleurotus cornucopiae'', containing two CBM67-like sequences in tandem with sequence identities with SaCBM67 of 25 and 35% for the N- and C-terminal modules, respectively, shows the highest affinity for ''N''-acetyl-ᴅ-galactosamine<cite>Fujimoto2013</cite>.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure of CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a characterized member of CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

File:SaCBM67 3.png

2018-11-15T07:52:35Z

Satoshi Kaneko:

Carbohydrate Binding Module Family 67

2018-11-15T07:07:46Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a [[GH78]] α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but it did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly, the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was observed <cite>Fujimoto2013</cite>.

== Structural Features ==
SaCBM67 is a ʟ-rhamnose binding module. The exo binding manner with shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, A, and C)<cite>Fujimoto2013</cite>. Domain D designated SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.

[[File:SaCBM67_3.png|thumb|300px|right|'''Figure 1.''' The structure of ʟ-rhamnose binding pocket of SaCBM67 [{{PDBlink}}3w5n 3W5N].]]

== Functionalities ==
Although SaCBM67 shows 2 times higher affinity for ʟ-rhamnose than ʟ-mannose<cite>Fujimoto2013</cite>. It binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually D179A and N180A mutant enzymes losted binding ability to ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide, these mutations did not influence activity against aryl-rhamnosides <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial [[GH78]] α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree<cite>Fujimoto2013</cite>. Although the calcium binding site is conserved in CBM67 members, these CBM67 members might show different sugar specificities because the ʟ-rhamnose binding residues in SaCBM67 are not retained in all the subfamilies. For example, the lectin from ''Pleurotus cornucopiae'', containing two CBM67-like sequences in tandem with sequence identities with SaCBM67 of 25 and 35% for the N- and C-terminal modules, respectively, shows the highest affinity for ''N''-acetyl-ᴅ-galactosamine<cite>Fujimoto2013</cite>.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure of CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a characterized member of CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-11-15T07:00:06Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a [[GH78]] α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but it did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly, the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was observed <cite>Fujimoto2013</cite>.

== Structural Features ==
SaCBM67 is a ʟ-rhamnose binding module. The exo binding manner with shallow binding site of SaCBM67 suggests it is a [[Carbohydrate-binding_modules#Types|type C]] CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain (domain A: catalytic module designated SaRha78<sub>CM</sub>) and five β-domains (domains N, D, E, F, A, and C)<cite>Fujimoto2013</cite>. Domain D designated SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a [[CBM32]], [[CBM35]], [[CBM36]], and [[CBM60]], which recognize their different ligands through either an exo- ([[CBM32]] and [[CBM35]]) or endo-mode ([[CBM36]] and [[CBM60]]) of binding. These CBMs all comprise a β-jellyroll structures and contain a second calcium atom that is integral to ligand recognition (which is absent in CBM32), in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (Figure 1, see also Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group points toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with the C-6 methyl group explains why SaCBM67 is also capable of binding to ʟ-mannose.

== Functionalities ==
Although SaCBM67 shows 2 times higher affinity for ʟ-rhamnose than ʟ-mannose<cite>Fujimoto2013</cite>. It binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually D179A and N180A mutant enzymes losted binding ability to ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide, these mutations did not influence activity against aryl-rhamnosides <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial [[GH78]] α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree<cite>Fujimoto2013</cite>. Although the calcium binding site is conserved in CBM67 members, these CBM67 members might show different sugar specificities because the ʟ-rhamnose binding residues in SaCBM67 are not retained in all the subfamilies. For example, the lectin from ''Pleurotus cornucopiae'', containing two CBM67-like sequences in tandem with sequence identities with SaCBM67 of 25 and 35% for the N- and C-terminal modules, respectively, shows the highest affinity for ''N''-acetyl-ᴅ-galactosamine<cite>Fujimoto2013</cite>.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure of CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a characterized member of CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-11T05:35:41Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

== Structural Features ==
SaCBM67 is a ʟ-rhamnose binding module. SaCBM67 is thus a type C CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain and five β-domains (domains N, D, E, F, A (catalytic module designated SaRha78<sub>CM</sub>), and C. Domain D designated SaCBM67 (P133-P297). SaCBM67 displays weak structural homology with a CBM32, CBM35, CBM36, and CBM60, which recognize their different ligands through either an exo- (CBM32 and CBM35) or endo-mode (CBM36 and CBM60) of binding. These CBMs all comprise a β-jellyroll structure and contain a second calcium atom that is integral to ligand recognition, in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (see Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group pointed toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with C-6 methyl group well explained why SaCBM67 also bind to ʟ-mannose.

== Functionalities ==
Although SaCBM67 showed 2 times higher affinity for ʟ-mannose than ʟ-rhamnose, it binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually mutant enzymes deleted calcium-mediated and direct hydrogen bonds with ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide (the mutantions did not influence activity against aryl-rhamnosides) <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial GH78 α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree. Although the calcium binding site is conserved in the CBM67, these CBM67 might show different sugar specificity because the ʟ-rhamnose binding residues in SaCBM67 are not retaining in the other CBM67 members. For example, the lectin from ''Pleurotus cornucopiae'' contains two CBM67-like sequences in tandem with sequence identities against SaCBM67 of 25 and 35% for the N- and C-terminal modules respectively, shows highest affinity against ''N''-acetyl-ᴅ-galactosamine.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T06:50:57Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

== Structural Features ==
SaCBM67 is ʟ-rhamnose binding module. SaCBM67 is thus a type C CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain and five β-domains (domains N, D, E, F, A (catalytic module designated SaRha78<sub>CM</sub>), and C. Domain D designated SaCBM67 (Pro133-Pro297). SaCBM67 displays weak structural homology with a CBM32, CBM35, CBM36, and CBM60, which recognize their different ligands through either an exo- (CBM32 and CBM35) or endo-mode (CBM36 and CBM60) of binding. These CBMs all comprise a β-jellyroll structure and contain a second calcium atom that is integral to ligand recognition, in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (see Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group pointed toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with C-6 methyl group well explained why SaCBM67 also bind to ʟ-mannose.

== Functionalities ==
Although SaCBM67 showed 2 times higher affinity for ʟ-mannose than ʟ-rhamnose, SaCBM67 binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually mutant enzymes deleted calcium-mediated and direct hydrogen bonds with ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide (the mutantions did not influence activity against aryl-rhamnosides) <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial GH78 α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree. Although the calcium binding site is conserved in the CBM67, these CBM67 might show different sugar specificity because the ʟ-rhamnose binding residues in SaCBM67 are not retaining in the other CBM67 members. For example, the lectin from ''Pleurotus cornucopiae'' contains two CBM67-like sequences in tandem with sequence identities against SaCBM67 of 25 and 35% for the N- and C-terminal modules respectively, shows highest affinity against ''N''-acetyl-ᴅ-galactosamine.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T06:49:41Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

== Structural Features ==
SaCBM67 is ʟ-rhamnose binding module. SaCBM67 is thus a type C CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain and five β-domains (domains N, D, E, F, A (catalytic module designated SaRha78<sub>CM</sub>), and C). Domain D designated SaCBM67 (Pro133-Pro297). SaCBM67 displays weak structural homology with a CBM32, CBM35, CBM36, and CBM60, which recognize their different ligands through either an exo- (CBM32 and CBM35) or endo-mode (CBM36 and CBM60) of binding. These CBMs all comprise a β-jellyroll structure and contain a second calcium atom that is integral to ligand recognition, in addition to a structural calcium (which is absent in CBM67). A central feature of the ʟ-rhamnose binding site in SaCBM67 (see Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound ʟ-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group pointed toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with C-6 methyl group well explained why SaCBM67 also bind to ʟ-mannose.

== Functionalities ==
Although SaCBM67 showed 2 times higher affinity for ʟ-mannose than ʟ-rhamnose, SaCBM67 binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually mutant enzymes deleted calcium-mediated and direct hydrogen bonds with ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide (the mutantions did not influence activity against aryl-rhamnosides) <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial GH78 α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree. Although the calcium binding site is conserved in the CBM67, these CBM67 might show different sugar specificity because the ʟ-rhamnose binding residues in SaCBM67 are not retaining in the other CBM67 members. For example, the lectin from ''Pleurotus cornucopiae'' contains two CBM67-like sequences in tandem with sequence identities against SaCBM67 of 25 and 35% for the N- and C-terminal modules respectively, shows highest affinity against ''N''-acetyl-ᴅ-galactosamine.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T06:44:24Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

== Structural Features ==
SaCBM67 is L-rhamnose binding module. SaCBM67 is thus a type C CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain and five β-domains (domains N, D, E, F, A (catalytic module designated SaRha78CM), and C). Domain D designated SaCBM67 (Pro133-Pro297). SaCBM67 displays weak structural homology with a CBM32, CBM35, CBM36, and CBM60, which recognize their different ligands through either an exo- (CBM32 and CBM35) or endo-mode (CBM36 and CBM60) of binding. These CBMs all comprise a β-jellyroll structure and contain a second calcium atom that is integral to ligand recognition, in addition to a structural calcium (which is absent in CBM67). A central feature of theL-rhamnose binding site in SaCBM67 (see Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound L-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group pointed toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with C-6 methyl groupwell explained why SaCBM67 also bind to L-mannose.

== Functionalities ==
Although SaCBM67 showed 2 times higher affinity for ʟ-mannose than ʟ-rhamnose, SaCBM67 binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually mutant enzymes deleted calcium-mediated and direct hydrogen bonds with ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide (the mutantions did not influence activity against aryl-rhamnosides) <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial GH78 α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree. Although the calcium binding site is conserved in the CBM67, these CBM67 might show different sugar specificity because the ʟ-rhamnose binding residues in SaCBM67 are not retaining in the other CBM67 members. For example, the lectin from ''Pleurotus cornucopiae'' contains two CBM67-like sequences in tandem with sequence identities against SaCBM67 of 25 and 35% for the N- and C-terminal modules respectively, shows highest affinity against ''N''-acetyl-ᴅ-galactosamine.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T06:43:32Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

''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 Armenta2017</cite>.

== Structural Features ==
SaCBM67 is L-rhamnose binding module. SaCBM67 is thus a type C CBM. SaRha78A (pdb: 3W5N) forms a multidomain structure comprised of six distinct domains, one α-domain and five β-domains (domains N, D, E, F, A (catalytic module designated SaRha78CM), and C). Domain D designated SaCBM67 (Pro133-Pro297). SaCBM67 displays weak structural homology with a CBM32, CBM35, CBM36, and CBM60, which recognize their different ligands through either an exo- (CBM32 and CBM35) or endo-mode (CBM36 and CBM60) of binding. These CBMs all comprise a β-jellyroll structure and contain a second calcium atom that is integral to ligand recognition, in addition to a structural calcium (which is absent in CBM67). A central feature of theL-rhamnose binding site in SaCBM67 (see Fig. 3C of <cite>Fujimoto2013</cite>) is a calcium ion that makes coordinate bonds with O3 and O4 of the sugar. The calcium interacts with SaCBM67 through D179, N180, N228, P233, and a water-mediated contact with S230. The bound L-rhamnose also makes direct hydrogen bonds with W203, N180, and D179 through O2, O3, and O4 atoms, respectively. The C-6 methyl group pointed toward a small hydrophobic pocket comprising W203, P233, P291 and W292. No direct interaction with C-6 methyl groupwell explained why SaCBM67 also bind to L-mannose.

== Functionalities ==
Although SaCBM67 showed 2 times higher affinity for ʟ-mannose than ʟ-rhamnose, SaCBM67 binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually mutant enzymes deleted calcium-mediated and direct hydrogen bonds with ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide (the mutantions did not influence activity against aryl-rhamnosides) <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial GH78 α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree. Although the calcium binding site is conserved in the CBM67, these CBM67 might show different sugar specificity because the ʟ-rhamnose binding residues in SaCBM67 are not retaining in the other CBM67 members. For example, the lectin from ''Pleurotus cornucopiae'' contains two CBM67-like sequences in tandem with sequence identities against SaCBM67 of 25 and 35% for the N- and C-terminal modules respectively, shows highest affinity against ''N''-acetyl-ᴅ-galactosamine.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T05:03:43Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

''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 Armenta2017</cite>.

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

== Functionalities ==
Although SaCBM67 showed 2 times higher affinity for ʟ-mannose than ʟ-rhamnose, SaCBM67 binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually mutant enzymes deleted calcium-mediated and direct hydrogen bonds with ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide (the mutantions did not influence activity against aryl-rhamnosides) <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial GH78 α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree. Although the calcium binding site is conserved in the CBM67, these CBM67 might show different sugar specificity because the ʟ-rhamnose binding residues in SaCBM67 are not retaining in the other CBM67 members. For example, the lectin from ''Pleurotus cornucopiae'' contains two CBM67-like sequences in tandem with sequence identities against SaCBM67 of 25 and 35% for the N- and C-terminal modules respectively, shows highest affinity against ''N''-acetyl-ᴅ-galactosamine.

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T04:59:08Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

''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 Armenta2017</cite>.

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

== Functionalities ==
Although SaCBM67 showed 2 times higher affinity for ʟ-mannose than ʟ-rhamnose, SaCBM67 binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually mutant enzymes deleted calcium-mediated and direct hydrogen bonds with ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide (the mutantions did not influence activity against aryl-rhamnosides) <cite>Fujimoto2013</cite>.

CBM67 members are distributed not only in many bacterial GH78 α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree. Although the calcium binding site is conserved in the CBM67, these CBM67 might show different sugar specificity because the ʟ-rhamnose binding residues in SaCBM67 are not retaining in the other CBM67 members. For example, the lectin from ''Pleurotus cornucopiae'' contains two CBM67-like sequences in tandem with sequence identities against SaCBM67 of 25 and 35% for the N- and C-terminal modules respectively, shows highest affinity against ''N''-acetyl-ᴅ-galactosamine.

''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
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T04:55:29Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

''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 Armenta2017</cite>.

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

== Functionalities ==
Although SaCBM67 showed 2 times higher affinity for ʟ-mannose than ʟ-rhamnose, SaCBM67 binds primarily to ʟ-rhamnose in biological systems because ʟ-mannose seldom exists in natural polysaccharides. Actually mutant enzymes deleted calcium-mediated and direct hydrogen bonds with ʟ-rhamnose caused a substantial reduction (∼50-fold) in activity against the ʟ-rhamnose-containing polysaccharide (the mutantions did not influence activity against aryl-rhamnosides).

CBM67 members are distributed not only in many bacterial GH78 α-ʟ-rhamnosidases, but also in some Basidiomycete lectins, family 1 pectate lyases, peptidases, and proteins of unknown functions. Protein alignment of candidate members of CBM67 identified five subfamilies within the constructed phylogenetic tree. Although the calcium binding site is conserved in the CBM67, these CBM67 might show different sugar specificity because the ʟ-rhamnose binding residues in SaCBM67 are not retaining in the other CBM67 members. For example, the lectin from ''Pleurotus cornucopiae'' contains two CBM67-like sequences in tandem with sequence identities against SaCBM67 of 25 and 35% for the N- and C-terminal modules respectively, shows highest affinity against ''N''-acetyl-ᴅ-galactosamine.

''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
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T02:47:41Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup> and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding to ʟ-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

''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 Armenta2017</cite>.

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

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

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T02:45:20Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from ''Streptomyces avermitilis'' (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a ''K<sub>a</sub>'' of 7.2 × 10<sup>3</sup> M<sup>−1</sup>and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, and free energy of binding Δ''G'' of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding tol-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

''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 Armenta2017</cite>.

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

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

== Family Firsts ==
;First Identified
:SaCBM67 from the ''S. avermitilis'' α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from ''Bacillus'' sp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T02:36:53Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from Streptomyces avermitilis (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement <cite>Fujimoto2013</cite>. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a Kaof 7.2 × 10<sup>3</sup> M<sup>−1</sup>and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, andfree energy of binding ΔG of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA <cite>Fujimoto2013</cite>. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand <cite>Fujimoto2013</cite>. No binding tol-galactose or ʟ-fucose was also observed <cite>Fujimoto2013</cite>.

''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 Armenta2017</cite>.

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

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

== Family Firsts ==
;First Identified
:SaCBM67 from the S. avermitilis α-l-rhamnosidase SaRha78A was the first member of the family to be identified and characterized <cite>Fujimoto2013</cite>.
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from Bacillussp. GL1 <cite>Cui2007</cite>, but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 <cite>Fujimoto2013</cite>.

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T02:34:12Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-ʟ-rhamnosidase from Streptomyces avermitilis (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement[<cite>Fujimoto2013</cite>]. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a Kaof 7.2 × 10<sup>3</sup> M<sup>−1</sup>and 3.6 × 10<sup>3</sup> M<sup>−1</sup>, andfree energy of binding ΔG of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA [<cite>Fujimoto2013</cite>]. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand [<cite>Fujimoto2013</cite>]. No binding tol-galactose or ʟ-fucose was also observed [<cite>Fujimoto2013</cite>].

''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 Armenta2017</cite>.

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

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

== Family Firsts ==
;First Identified
:SaCBM67 from the S. avermitilis α-l-rhamnosidase SaRha78A was the first member of the family to be identified and characterized [<cite>Fujimoto2013</cite>].
;First Structural Characterization
:The first structure in CBM67 is a module involved in BsRhaB from Bacillussp. GL1 [<cite>Cui2007</cite>], but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 [<cite>Fujimoto2013</cite>].

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T02:24:48Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-l-rhamnosidase from Streptomyces avermitilis(SaRha78A) revealed a l-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement. SaCBM67 bound l-rhamnose and l-mannose with a Kaof 7.2 × 103M−1and 3.6 × 103M−1, andfree energy of binding ΔG of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to l-rhamnose in the presence of 5 mM EDTA. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds withl-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand. No binding tol-galactose or l-fucose was also observed.

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 Armenta2017</cite>.

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

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

== Family Firsts ==
;First Identified
:Insert archetype here, possibly including ''very brief'' synopsis.SaCBM67 from the S. avermitilis α-l-rhamnosidase SaRha78A was the first member of the family to be identified and characterized [1].
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.The first structure in CBM67 is a module involved in BsRhaB from Bacillussp. GL1 [2], but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 [1].

== References ==
<biblio>
#Fujimoto2013 pmid=23486481
#Cui2007 pmid=17936784
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T02:18:53Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Harry Gilbert^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM67.html
|}
</div>


== Ligand specificities ==
The sugar binding structure of a GH78 α-l-rhamnosidase from Streptomyces avermitilis(SaRha78A) revealed a l-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement. SaCBM67 bound l-rhamnose and l-mannose with a Kaof 7.2 × 103M−1and 3.6 × 103M−1, andfree energy of binding ΔG of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to l-rhamnose in the presence of 5 mM EDTA. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds withl-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand. No binding tol-galactose or l-fucose was also observed.

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 Armenta2017</cite>.

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

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

== Family Firsts ==
;First Identified
:Insert archetype here, possibly including ''very brief'' synopsis.SaCBM67 from the S. avermitilis α-l-rhamnosidase SaRha78A was the first member of the family to be identified and characterized [1].
;First Structural Characterization
:Insert archetype here, possibly including ''very brief'' synopsis.The first structure in CBM67 is a module involved in BsRhaB from Bacillussp. GL1 [2], but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 [1].

== 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. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
#Boraston2004 pmid=15214846
#Hashimoto2006 pmid=17131061
#Shoseyov2006 pmid=16760304
#Guillen2010 pmid=19908036
#Armenta2017 pmid=28547780
</biblio>

[[Category:Carbohydrate Binding Module Families|CBM067]]

Carbohydrate Binding Module Family 67

2018-06-10T02:17:46Z

Satoshi Kaneko:

User:Satoshi Kaneko

2018-02-20T04:16:25Z

Satoshi Kaneko:

Satoshi Kaneko is a professor at Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus located in Okinawa island, Japan. Before he move to Okinawa, he was an Senior Researcher in the Food Biotechnology Division at the National Food Research Institute (NFRI) in Tsukuba Japan. He received his Ph.D. from University of Tsukuba. His research interests are the structure-function relationships of hemicellulases.
[[File:Satoshi Kaneko.jpg]]
[[Category:Contributors|Kaneko, Satoshi]]

File:Satoshi Kaneko.jpg

2018-02-20T04:15:02Z

Satoshi Kaneko: Satoshi Kaneko uploaded a new version of File:Satoshi Kaneko.jpg

File:Satoshi Kaneko.jpg

2018-02-20T04:06:28Z

Satoshi Kaneko: Satoshi Kaneko uploaded a new version of File:Satoshi Kaneko.jpg

File:Satoshi Kaneko.jpg

2018-02-20T04:00:21Z

Satoshi Kaneko: Satoshi Kaneko uploaded a new version of File:Satoshi Kaneko.jpg

User:Satoshi Kaneko

2018-02-20T03:56:49Z

Satoshi Kaneko:

Satoshi Kaneko is a professor at Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus located in Okinawa island, Japan. Before he move to Okinawa, he was an Senior Researcher in the Food Biotechnology Division at the National Food Research Institute (NFRI) in Tsukuba Japan. He received his Ph.D. from University of Tsukuba. His research interests are the structure-function relationships of hemicellulases. [[File:Satoshi Kaneko.jpg]]
[[Category:Contributors|Kaneko, Satoshi]]

File:Satoshi Kaneko.jpg

2018-02-20T03:52:03Z

Satoshi Kaneko:

User:Satoshi Kaneko

2018-02-20T03:30:27Z

Satoshi Kaneko:

User:Satoshi Kaneko

2018-02-20T03:28:02Z

Satoshi Kaneko:

User:Satoshi Kaneko

2018-02-20T02:58:43Z

Satoshi Kaneko:

Glycoside Hydrolase Family 79

2012-03-09T07:03:27Z

Satoshi Kaneko:

{{CuratorApproved}}
* [[Author]]: ^^^Hitomi Ichinose^^^ and ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Satoshi Kaneko^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH79'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH79.html
|}
</div>


== Substrate specificities ==
Family GH79 enzymes are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (E.C. 3.2.1.31) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (E.C. 3.2.1.-) <cite> Kuroyama2001 </cite>, baicalin β-glucuronidase (E.C. 3.2.1.167) <cite> Sasaki2000 </cite>, heparanase (E.C. 3.2.1.-) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (E.C. 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.
Some β-glucuronidases have been shown to release both glucuronic acid (GlcA) and 4-''O''-methyl-GlcA from arabinogalactan proteins <cite> Kuroyama2001 Konishi2008 </cite>. The ''Aspergillus niger'' enzyme shows high activity for 4-''O''-methyl-GlcA residues <cite> Kuroyama2001 </cite>. ''Scutellaria baicalensis'' β-glucuronidase hydrolyzes baicalein 7-''O''-β-glucuronide, which is a major flavone of ''S. baicalensis'' <cite> Sasaki2000 </cite> Heparanase is an endo-β-glucuronidase that degrades heparan sulfate side chains of heparan sulfate proteoglycans. Heparanases are found in mammals such as human, mouse (''Mus musculus''), rat (''Rattus norvegicus''), cattle (''Bos indicus''), and chicken (''Gallus gallus'').

== Kinetics and Mechanism ==
GH79 β-glucuronidases are retaining enzymes, as first demonstrated by proton-NMR studies of the hydrolysis of p-nitrophenyl β-glucuronide by a β-glucuronidase from ''Acidobacterium capsulatum'' <cite> Michikawa2012 </cite>.

== Catalytic Residues ==
The catalytic residues were first identified in the ''A. capsulatum'' β-glucuronidase as Glu173 (acid/base) and Glu287 (nucleophile) by trapping of the 2-fluoroglucuronyl-enzyme intermediate and the mutagenesis studies <cite> Michikawa2012 </cite>.

== Three-dimensional structures ==
The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)8 TIM-barrel fold as members of clan GH-A.

== Family Firsts ==
;First stereochemistry determination: ''Acidobacterium capsulatum'' β-glucuronidase by 1H-NMR <cite> Michikawa2012 </cite>.
;First catalytic nucleophile identification: ''A. capsulatum'' β-glucuronidase by 2-fluoroglucuroic acid labeling and the mutagenesis study <cite> Michikawa2012 </cite>.
;First general acid/base residue identification: ''A. capsulatum'' β-glucuronidase by structural identification and the mutagenesis study <cite> Michikawa2012 </cite>.
;First 3-D structure: ''A. capsulatum'' β-glucuronidase <cite> Michikawa2012 </cite>.

== References ==
<biblio>
#Eudes2008 pmid=18667448
#Kuroyama2001 pmid=11423108
#Konishi2008 pmid=18377882
#Sasaki2000 pmid=10858442
#Michikawa2012 Michikawa M, Ichinose H, Momma M, Biely P, Jongkees S, Yoshida M, Kotake T, Tsumuraya Y, Withers S, Fujimoto Z, Kaneko S. ''Structural and biochemical characterization of glycoside hydrolase family 79 β-glucuronidase from Acidobacterium capsulatum.'' J. Biol. Chem. in press. PMID=22367201
#Vlodavsky1999 pmid=10395325
#Toyoshima1999 pmid=10446189
#Kussie1999 pmid=10405343
#Hulett1999 pmid=10395326
#Fairbanks1999 pmid=10514423
#Nardella2004 pmid=14967027
</biblio>

[[Category:Glycoside Hydrolase Families|GH079]]

Glycoside Hydrolase Family 79

2012-03-09T06:55:41Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Hitomi Ichinose^^^ and ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Satoshi Kaneko^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH79'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH79.html
|}
</div>


== Substrate specificities ==
Family GH79 enzymes are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (E.C. 3.2.1.31) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (E.C. 3.2.1.-) <cite> Kuroyama2001 </cite>, baicalin β-glucuronidase (E.C. 3.2.1.167) <cite> Sasaki2000 </cite>, heparanase (E.C. 3.2.1.-) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (E.C. 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.
Some β-glucuronidases have been shown to release both glucuronic acid (GlcA) and 4-''O''-methyl-GlcA from arabinogalactan proteins <cite> Kuroyama2001 Konishi2008 </cite>. The ''Aspergillus niger'' enzyme shows high activity for 4-''O''-methyl-GlcA residues <cite> Kuroyama2001 </cite>. ''Scutellaria baicalensis'' β-glucuronidase hydrolyzes baicalein 7-''O''-β-glucuronide, which is a major flavone of ''S. baicalensis'' <cite> Sasaki2000 </cite> Heparanase is an endo-β-glucuronidase that degrades heparan sulfate side chains of heparan sulfate proteoglycans. Heparanases are found in mammals such as human, mouse (''Mus musculus''), rat (''Rattus norvegicus''), cattle (''Bos indicus''), and chicken (''Gallus gallus'').

== Kinetics and Mechanism ==
GH79 β-glucuronidases are retaining enzymes, as first demonstrated by proton-NMR studies of the hydrolysis of p-nitrophenyl β-glucuronide by a β-glucuronidase from ''Acidobacterium capsulatum'' <cite> Michikawa2012 </cite>.

== Catalytic Residues ==
The catalytic residues were first identified in the ''A. capsulatum'' β-glucuronidase as Glu173 (acid/base) and Glu287 (nucleophile) by trapping of the 2-fluoroglucuronyl-enzyme intermediate and the mutagenesis studies <cite> Michikawa2012 </cite>.

== Three-dimensional structures ==
The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)8 TIM-barrel fold as members of clan GH-A.

== Family Firsts ==
;First stereochemistry determination: ''Acidobacterium capsulatum'' β-glucuronidase by 1H-NMR <cite> Michikawa2012 </cite>.
;First catalytic nucleophile identification: ''A. capsulatum'' β-glucuronidase by 2-fluoroglucuroic acid labeling and the mutagenesis study <cite> Michikawa2012 </cite>.
;First general acid/base residue identification: ''A. capsulatum'' β-glucuronidase by structural identification and the mutagenesis study <cite> Michikawa2012 </cite>.
;First 3-D structure: ''A. capsulatum'' β-glucuronidase <cite> Michikawa2012 </cite>.

== References ==
<biblio>
#Eudes2008 pmid=18667448
#Kuroyama2001 pmid=11423108
#Konishi2008 pmid=18377882
#Sasaki2000 pmid=10858442
#Michikawa2012 Michikawa M, Ichinose H, Momma M, Biely P, Jongkees S, Yoshida M, Kotake T, Tsumuraya Y, Withers S, Fujimoto Z, Kaneko S. ''Structural and biochemical characterization of glycoside hydrolase family 79 β-glucuronidase from Acidobacterium capsulatum.'' J. Biol. Chem. in press. PMID=22367201
#Vlodavsky1999 pmid=10395325
#Toyoshima1999 pmid=10446189
#Kussie1999 pmid=10405343
#Hulett1999 pmid=10395326
#Fairbanks1999 pmid=10514423
#Nardella2004 pmid=14967027
</biblio>

[[Category:Glycoside Hydrolase Families|GH079]]

Glycoside Hydrolase Family 79

2012-03-09T06:44:17Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Hitomi Ichinose^^^ and ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Satoshi Kaneko^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH79'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH79.html
|}
</div>


== Substrate specificities ==
Family GH79 enzymes are found widely distributed in bacteria and eukaryota including fungi, plants, and animals. The characterized activities of this family include β-glucuronidase (E.C. 3.2.1.31) <cite> Eudes2008 </cite>, β-4-''O''-methyl-glucuronidase (E.C. 3.2.1.-) <cite> Kuroyama2001 </cite>, baicalin β-glucuronidase (E.C. 3.2.1.167) <cite> Sasaki2000 </cite>, heparanase (E.C. 3.2.1.-) <cite> Vlodavsky1999 Toyoshima1999 Kussie1999 Hulett1999 Fairbanks1999 </cite> and hyaluronidase (E.C. 3.2.1.-) <cite> Nardella2004 </cite>. GH79s are involved in the metabolism of proteoglycans, such as heparan sulfate proteoglycan, chondroitin sulfate proteoglycan, and hyaluronan from animals and arabinogalactan-proteins from higher plants.
Some β-glucuronidases have been shown to release both glucuronic acid (GlcA) and 4-''O''-methyl-GlcA from arabinogalactan proteins <cite> Kuroyama2001 Konishi2008 </cite>. The ''Aspergillus niger'' enzyme shows high activity for 4-''O''-methyl-GlcA residues <cite> Kuroyama2001 </cite>. ''Scutellaria baicalensis'' β-glucuronidase hydrolyzes baicalein 7-''O''-β-glucuronide, which is a major flavone of ''S. baicalensis'' <cite> Sasaki2000 </cite> Heparanase is an endo-β-glucuronidase that degrades heparan sulfate side chains of heparan sulfate proteoglycans. Heparanases are found in mammals such as human, mouse (''Mus musculus''), rat (''Rattus norvegicus''), cattle (''Bos indicus''), and chicken (''Gallus gallus'').

== Kinetics and Mechanism ==
GH79 β-glucuronidases are retaining enzymes, as first demonstrated by proton-NMR studies of the hydrolysis of p-nitrophenyl β-glucuronide by a β-glucuronidase from ''Acidobacterium capsulatum'' <cite> Michikawa2012 </cite>.

== Catalytic Residues ==
The catalytic residues were first identified in the ''A. capsulatum'' β-glucuronidase as Glu173 (acid/base) and Glu287 (nucleophile) by trapping of the 2-fluoroglucuronyl-enzyme intermediate and the mutagenesis studies <cite> Michikawa2012 </cite>.

== Three-dimensional structures ==
The three-dimensional structure of ''A. capsulatum'' β-glucuronidase solved using X-ray crystallography represented the first structure of an enzyme of GH79 <cite> Michikawa2012 </cite>. The catalytic domain of the enzyme is a (β/α)8 TIM-barrel fold as members of clan GH-A.

== Family Firsts ==
;First stereochemistry determination: ''Acidobacterium capsulatum'' β-glucuronidase by 1H-NMR <cite> Michikawa2012 </cite>.
;First catalytic nucleophile identification: ''A. capsulatum'' β-glucuronidase by 2-fluoroglucuroic acid labeling and the mutagenesis study <cite> Michikawa2012 </cite>.
;First general acid/base residue identification: ''A. capsulatum'' β-glucuronidase by structural identification and the mutagenesis study <cite> Michikawa2012 </cite>.
;First 3-D structure: ''A. capsulatum'' β-glucuronidase <cite> Michikawa2012 </cite>.

== References ==
<biblio>
#Eudes2008 pmid=18667448
#Kuroyama2001 pmid=11423108
#Konishi2008 pmid=18377882
#Sasaki2000 pmid=10858442
#Michikawa2012 PMID=22367201
#Vlodavsky1999 pmid=10395325
#Toyoshima1999 pmid=10446189
#Kussie1999 pmid=10405343
#Hulett1999 pmid=10395326
#Fairbanks1999 pmid=10514423
#Nardella2004 pmid=14967027
</biblio>

[[Category:Glycoside Hydrolase Families|GH079]]

Glycoside Hydrolase Family 115

2011-05-12T07:33:56Z

Satoshi Kaneko:

{{CuratorApproved}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Satoshi Kaneko^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH115'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH115.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolases of this family display alpha-glucuronidase activity. The enzymes possible to release 4-O-methyl D-glucuronic acid from polymeric xylans. The substrate specificity could be distinguished from GH67 enzymes. In contrast to GH67 enzymes which only cleave glucuronosyl linkage at the non-reducing end of xylooligosaccharides, GH115 enzymes remove glucuronic acid from the both terminal and internal regions of xylooligosaccharides and xylans. This kind of substrate specificty firstly demonstrated by an alpha-glucuronidase purified from Thermoascus aurantiacus <cite>Khandke1989</cite> and N-terminal amino acid sequence of Schizophyllum commune firstly provided <cite>Tenkanen2000</cite>. In spite of the N-terminal amino acid sequence of Pichia stipitis did not show significant similarity with the sequence of S. commune, the information lead to find full amino acid sequence and establish this family <cite>Ryabova2009</cite>. It has been demonstrated that these enzymes release 4-O-methyl D-glucuronic acid, the enzyme from Streptomyces pristinaespiralis produced the both 4-O-methyl D-glucuronic acid and non methylated D-glucuronic acid as the reaction product <cite>Fujimoto2011</cite>.

== Kinetics and Mechanism ==
Using 1H NMR spectroscopy and reduced aldopentaouronic acid(MeGlcA3Xyl4-ol) as a substrate, it was demonstrated that both the enzymes from S. commune and P. stipitis releasing 4-O-methyl-D-glucuronic acid (MeGlcA) as its beta-anomer, suggesting a single displacement mechanism <cite>Kolenova2010</cite>.

== Catalytic Residues ==
Not identified.

== Three-dimensional structures ==
No 3D-structure is solved for this family of enzyme.

== Family Firsts ==
;First stereochemistry determination:1H NMR demonstrated that the released 4-methyl-D-glucuronic acid was a beta anomer and thus that the enzyme is an inverter <cite>Kolenova2010</cite>.
;First catalytic nucleophile identification:unproved.
;First general acid/base residue identification:unproved.
;First 3-D structure:Just crystallization of S. pristinaespiralis enzyme is reported <cite>Fujimoto2011</cite>.

== References ==
<biblio>
#Khandke1989 pmid=2802623
#Tenkanen2000 pmid=10725538
#Ryabova2009 pmid=19344716
#Kolenova2010 Kolenová K, Ryabova O, Vrsanská M, Biely P. ''Inverting character of family GH115 α-glucuronidases.'' FEBS Lett. 2010 Sep 24;584(18):4063-4068. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out:'' [http://dx.doi.org/10.1016/j.febslet.2010.08.031 DOI:10.1016/j.febslet.2010.08.031] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20804758 PMID: 20804758]
#Fujimoto2011 Fujimoto Z, Ichinose H, Biely P, Kaneko S. ''Crystallization and preliminary crystallographic analysis of the glycoside hydrolase family 115 α-glucuronidase from Streptomyces pristinaespiralis.'' Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jan 1;67(Pt 1):68-71. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out:'' [http://dx.doi.org/10.1107/S1744309110043721 DOI:10.1107/S1744309110043721] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21206027 PMID: 21206027]
</biblio>

[[Category:Glycoside Hydrolase Families|GH115]]

Glycoside Hydrolase Family 115

2011-05-12T02:20:19Z

Satoshi Kaneko:

Glycoside Hydrolase Family 115

2011-05-12T01:50:09Z

Satoshi Kaneko:

Glycoside Hydrolase Family 115

2011-05-12T01:41:41Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Satoshi Kaneko^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH115'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH115.html
|}
</div>


== Substrate specificities ==
Glycoside hydrolases of this family display alpha-glucuronidase activity. The enzymes possible to release 4-O-methyl D-glucuronic acid from polymeric xylans. The substrate specificity could be distinguished from GH67 enzymes. In contrast to GH67 enzymes which only cleave glucuronosyl linkage at the non-reducing end of xylooligosaccharides, GH115 enzymes remove glucuronic acid from the both terminal and internal regions of xylooligosaccharides and xylans. This kind of substrate specificty firstly demonstrated by an alpha-glucuronidase purified from Thermoascus aurantiacus <cite>Khandke1989</cite> and N-terminal amino acid sequence of Schizophyllum commune firstly provided <cite>2</cite>. In spite of the N-terminal amino acid sequence of Pichia stipitis did not show significant similarity with the sequence of S. commune, the information lead to find full amino acid sequence and establish this family <cite>3</cite>. It has been demonstrated that these enzymes release 4-O-methyl D-glucuronic acid, the enzyme from Streptomyces pristinaespiralis produced the both 4-O-methyl D-glucuronic acid and non methylated D-glucuronic acid as the reaction product <cite>4</cite>.

This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>StickWilliams</cite>. References that are not in PubMed can be typed in by hand <cite>Sinnott1990</cite>.

== Kinetics and Mechanism ==
Using 1H NMR spectroscopy and reduced aldopentaouronic acid(MeGlcA3Xyl4-ol) as a substrate, it was demonstrated that both the enzymes from S. commune and P. stipitis releasing 4-O-methyl-D-glucuronic acid (MeGlcA) as its beta-anomer, suggesting a single displacement mechanism [5].

== Catalytic Residues ==
Not identified.

== Three-dimensional structures ==
No 3D-structure is solved for this family of enzyme.

== Family Firsts ==
; Normal 0 0 2 false false false EN-US JA X-NONE First stereochemistry determination:1H NMR demonstrated that the released 4-methyl-D-glucuronic acid was a beta anomer and thus that the enzyme is an inverter <cite>Kolenová2010</cite>.
;First catalytic nucleophile identification:unproved.
;First general acid/base residue identification:unproved.
;First 3-D structure:Just crystallization of S. pristinaespiralis enzyme is reported <cite>Fujimoto2011</cite>.

== References ==
<biblio>
#Khandke1989 pmid=2082623
# Normal 0 0 2 false false false EN-US JA X-NONE Tenkanen2000 pmid= Normal 0 0 2 false false false EN-US JA X-NONE 10725538
# Normal 0 0 2 false false false EN-US JA X-NONE Ryabova2009 pmid= Normal 0 0 2 false false false EN-US JA X-NONE 19344716
# Normal 0 0 2 false false false EN-US JA X-NONE Fujimoto2011 pmid= Normal 0 0 2 false false false EN-US JA X-NONE 21206027
# Normal 0 0 2 false false false EN-US JA X-NONE Kolenová2010 pmid= Normal 0 0 2 false false false EN-US JA X-NONE 20804758
</biblio>

[[Category:Glycoside Hydrolase Families|GH115]]

Glycoside Hydrolase Family 115

2011-05-12T01:33:17Z

Satoshi Kaneko:

Glycoside Hydrolase Family 115

2011-05-12T01:25:22Z

Satoshi Kaneko:

{{UnderConstruction}}
* [[Author]]: ^^^Satoshi Kaneko^^^
* [[Responsible Curator]]: ^^^Satoshi Kaneko^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH115'''
|-
|'''Clan'''
|GH-x
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH115.html
|}
</div>


== Substrate specificities ==
Normal 0 0 2 false false false EN-US JA X-NONE Glycoside hydrolases of this family display alpha-glucuronidase activity. The enzymes possible to release 4-O-methyl D-glucuronic acid from polymeric xylans. The substrate specificity could be distinguished from GH67 enzymes. In contrast to GH67 enzymes which only cleave glucuronosyl linkage at the non-reducing end of xylooligosaccharides, GH115 enzymes remove glucuronic acid from the both terminal and internal regions of xylooligosaccharides and xylans. This kind of substrate specificty firstly demonstrated by an alpha-glucuronidase purified from Thermoascus aurantiacus [1] and N-terminal amino acid sequence of Schizophyllum commune firstly provided [2]. In spite of the N-terminal amino acid sequence of Pichia stipitis did not show significant similarity with the sequence of S. commune, the information lead to find full amino acid sequence and establish this family [3]. It has been demonstrated that these enzymes release 4-O-methyl D-glucuronic acid, the enzyme from Streptomyces pristinaespiralis produced the both 4-O-methyl D-glucuronic acid and non methylated D-glucuronic acid as the reaction product [4].

This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>StickWilliams</cite>. References that are not in PubMed can be typed in by hand <cite>Sinnott1990</cite>.

== Kinetics and Mechanism ==
Normal 0 0 2 false false false EN-US JA X-NONE

Using 1H NMR spectroscopy and reduced aldopentaouronic acid

(MeGlcA3Xyl4-ol) as a substrate, it was demonstrated that both the enzymes from S. commune and P. stipitis releasing 4-O-methyl-D-glucuronic acid (MeGlcA) as its beta-anomer, suggesting a single displacement mechanism [5].

== Catalytic Residues ==
Normal 0 0 2 false false false EN-US JA X-NONE Not identified.

== Three-dimensional structures ==
Normal 0 0 2 false false false EN-US JA X-NONE No 3D-structure is solved for this family of enzyme.

== Family Firsts ==
Normal 0 0 2 false false false EN-US JA X-NONE 1H NMR demonstrated that the released 4-methyl-D-glucuronic acid was a beta anomer and thus that the enzyme is an inverter [5]. <cite>Comfort2007</cite>.
;First catalytic nucleophile identification: Normal 0 0 2 false false false EN-US JA X-NONE unproved <cite>Sinnott1990</cite>.
;First general acid/base residue identification: Normal 0 0 2 false false false EN-US JA X-NONE unproved <cite>He1999</cite>.
;First 3-D structure: Normal 0 0 2 false false false EN-US JA X-NONE Just crystallization of S. pristinaespiralis enzyme is reported [4]. <cite>StickWilliams</cite>.

== References ==
<biblio>
#Comfort2007 pmid=17323919
#He1999 pmid=9312086
#StickWilliams isbn=978-0-240-52118-3
#Sinnott1990 Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]
</biblio>

[[Category:Glycoside Hydrolase Families|GH115]]

User:Satoshi Kaneko

2008-09-22T11:40:01Z

Satoshi Kaneko: New page: This is the user page of Satoshi Kaneko, Ph.D. I am an Senior Researcher in the Food Biotechnology Division at the National Food Research Institute (NFRI) in Tsukuba Japan

This is the user page of Satoshi Kaneko, Ph.D. I am an Senior Researcher in the Food Biotechnology Division at the National Food Research Institute (NFRI) in Tsukuba Japan

Glycoside Hydrolase Family 43

2008-09-22T11:34:27Z

Satoshi Kaneko: /* Family Firsts */

* Author: [[User:SatoshiKaneko|Satoshi Kaneko]]
* Responsible Editor: [[User:hbrumer3|Harry Brumer]]
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH43'''
|-
|'''Clan'''
|GH-F
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH43.html
|}
</div>

== Substrate specificities ==

== Kinetics and Mechanism ==

== Catalytic Residues ==

== Three-dimensional structures ==

== Family Firsts ==
;First sterochemistry determination:
;First catalytic nucleophile identification:
;First general acid/base residue identification:
;First 3-D structure: alpha-L-Arabinanase from ''Cellvibrio japonicus'' <cite>1</cite>.

== References ==
<biblio>
#1 pmid=12198486
</biblio>

[[Category:Glycoside Hydrolase Families]]

Glycoside Hydrolase Family 43

2008-09-22T11:33:12Z

Satoshi Kaneko:

* Author: [[User:SatoshiKaneko|Satoshi Kaneko]]
* Responsible Editor: [[User:hbrumer3|Harry Brumer]]
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH43'''
|-
|'''Clan'''
|GH-F
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH43.html
|}
</div>

== Substrate specificities ==

== Kinetics and Mechanism ==

== Catalytic Residues ==

== Three-dimensional structures ==

== Family Firsts ==
;First sterochemistry determination:
;First catalytic nucleophile identification:
;First general acid/base residue identification:
;First 3-D structure: alpha-L-Arabinanase from ''Cellvibrio japonicus'' <cite>12/cite>.

== References ==
<biblio>
#1 pmid=12198486
</biblio>

[[Category:Glycoside Hydrolase Families]]

Glycoside Hydrolase Family 43

2008-09-22T11:32:19Z

Satoshi Kaneko:

* Author: [[User:SatoshiKaneko|Satoshi Kaneko]]
* Responsible Editor: [[User:hbrumer3|Harry Brumer]]
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH43'''
|-
|'''Clan'''
|GH-F
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH43.html
|}
</div>

== Substrate specificities ==

== Kinetics and Mechanism ==

== Catalytic Residues ==

== Three-dimensional structures ==

== Family Firsts ==
;First sterochemistry determination:
;First catalytic nucleophile identification:
;First general acid/base residue identification:
;First 3-D structure: alpha-L-Arabinanase from ''Cellvibrio japonicus'' <cite>12</cite>.

== References ==
<biblio>
#12 pmid=12198486
</biblio>

[[Category:Glycoside Hydrolase Families]]

Glycoside Hydrolase Family 43

2008-09-22T11:17:36Z

Satoshi Kaneko:

* Author: [[User:SatoshiKaneko|Satoshi Kaneko]]
* Responsible Editor: [[User:hbrumer3|Harry Brumer]]
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH43'''
|-
|'''Clan'''
|GH-F
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH43.html
|}
</div>

== Substrate specificities ==

== Kinetics and Mechanism ==

== Catalytic Residues ==

== Three-dimensional structures ==

== Family Firsts ==
;First sterochemistry determination: Cite some reference here, with a ''short'' explanation <cite>1</cite>.
;First catalytic nucleophile identification:
;First general acid/base residue identification:
;First 3-D structure:

== References ==
<biblio>
#1 pmid=17323919

</biblio>

[[Category:Glycoside Hydrolase Families]]