CAZypedia - User contributions [en-ca]

File:Cbm13 overview.png

2025-10-30T08:08:36Z

Lauren McKee: Structural features of CBM13 proteins.

== Summary ==
Structural features of CBM13 proteins.

Carbohydrate Binding Module Family 92

2024-05-16T12:42:23Z

Lauren McKee: Fixed an error in the legend to figure 2.

{{CuratorApproved}}
* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]] and [[User:Lauren McKee|Lauren McKee]]

* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]

----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM92.html
|}
</div>


== Ligand specificities ==
The first published CBM92 domain, and founding member of the CBM92 family, is the Cgk16A-CBM92 from the marine bacterium ''Wenyingzhuangia aestuarii'' OF219 <cite>Mei2022</cite>. The CBM92 bound specifically to the red algal polysaccharide carrageenan, a substrate of the appended [[GH16]] enzyme domain. It was incapable of binding to other polysaccharide components in red algae including agarose, porphyran, and funoran <cite>Mei2022</cite>. Meanwhile, the CBM92 displayed no affinity to several anionic polysaccharides, namely pectin, chondroitin sulfates, dermatan sulfate, and sulfated fucans <cite>Mei2022</cite>. The Cgk16A-CBM92 showed no significant difference in the affinity to κ- and ι-carrageenan.

An earlier paper had demonstrated carbohydrate binding by a so-called Bacterial Fascin-like Domain (BFLD) within the [[GH16]] β−1,3-glucanase LamC from a myxobacterial ''Corallococcus'' species. Affinity gel electrophoresis showed that the domain, now recognized as a [http://www.cazy.org/CBM92.html CBM92 domain] could bind to β−1,3-glucans <cite>Zhou2017</cite>. Later, Lu et al showed binding to β-1,6-glucan by a CBM92 domain found within ''Cp''Glu30A, a [[GH30]] β-1,6-glucanase <cite>Lu2023</cite>. Binding to the Glc- β-1,6-Glc structure found in pustulan, laminarin, scleroglucan, and yeast β-glucan has since been demonstrated for 12 additional members of family CBM92, none of which were able to bind carrageenan <cite>Hao2024</cite>.

== Structural Features ==
[[File:CBM92logo.png|thumb|400px|right|'''Figure 1'''. A consensus sequence logo generated from an alignment of 818 CBM92 domain sequences, including all carrageenan- and β-glucan binders characterised as of May 2024.]]

Several conserved residues (e.g., Phe-70, Arg-72, and Phe-75) were discovered through the multiple sequence alignments of Cgk16A-CBM92 and its close homologs <cite>Mei2022</cite>, which were suggested to be critical for the ligand binding of that CBM. Phylogenetic analysis by Hao et al later showed that the homologs of Cgk16A-CBM92 represent a small sub-group within the CBM92 family (Fig. 1) <cite>Hao2024</cite>. In most other members of CBM92, there are three apparent binding sites identified by a conserved WExF sequence motif. The Trp of this motif is the principal sugar-binding residue, as evidenced by a site-directed mutagenesis study that could abolish binding by altering these residues to Ala <cite>Hao2024</cite>. The same paper also showed that wild-type proteins with fewer Trp-containing binding sites generally showed weaker binding to polysaccharide ligand <cite>Hao2024</cite>. A conserved CNR motif is found just to the N-terminal of the WExF sequence (Fig. 1). Structural analysis revealed that the Arg of this trio contributes to ligand binding, although it is absent in some binding sites in some proteins <cite>Hao2024</cite>.

[[File:CBM92structure.png|thumb|400px|right|'''Figure 2'''. '''a''' Overall structure of ''Cp''CBM92B with the subdomains distinctly coloured and its ligand binding Trp and Glu residues shown as sticks. '''b''' The β-subdomain of ''Cp''CBM92B in complex with glucose. '''c''' Overlay of the ''Cp''CBM92A and -B subdomains showing sequence conservation within all putative binding sites. Single letter residue codes are colored based on the subdomains shown in panel '''a''' , and are labelled for subdomains ⍺/β/γ, in that order, with the ''Cp''CBM92A codes shown above those for ''Cp''CBM92B. Figure generated by [[User:Scott Mazurkewich| Scott Mazurkewich]] ]]

The crystal structures of ''Cp''CBM92A and ''Cp''CBM92B reveal a β-trefoil structure comprised of 12 β-strands arranged into 3 subdomains (⍺, β, and γ), like the β-trefoil domains found in Fascin and [[CBM13]] proteins (Fig.2). Soaking experiments of ''Cp''CBM92B crystals with glucose, gentiobiose, and sophorose revealed a binding cleft within each subdomain comprising a Trp-Glu binding pair, contributed by the WExF motifs <cite>Hao2024</cite>. Ligand-bound structures suggest the potential for end-on binding to glucose and glucan oligo- or polysaccharides of potentially any linkage, but also reveal the possibility for extensions from both the O1 and O6 positions, enabling the observed mid-chain binding to a β−1,6-glucan such as pustulan, or to β-1,6-linked glucosyl substitutions in scleroglucan or laminarin.

== Functionalities ==
[[File:Figure 1.png|thumb|400px|right|'''Figure 3. Domain architecture of the κ-carrageenase Cgk16A. '''The enzyme consists of a signal peptide (1-20 amino acids), a GH16 domain (21-347 amino acids), a CBM92 domain (viz., Cgk16A-CBM92; 378-490 amino acids) and a C-terminal Sorting domain (516-581 amino acids).''' ]]

In the natural context, Cgk16A-CBM92 is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite> (Fig. 3). It thus might maintain the enzyme near its substrate to improve the enzymatic activity via the proximity effect. The same observation was made for a β-1,6-glucan-binding CBM92 found appended to a [[GH30]] β-1,6-glucanase enzyme from the environmental bacterium ''Chitinophaga pinensis'' <cite>Lu2023</cite>.

Members of the CBM92 family are present in different glycoside hydrolase (GH) family sequences, e.g., [[GH16]]_17, [[GH5]]_46, [[GH5]]_54, [[GH18]], [[GH19]], [[GH30]], and [[GH95]]. According to the [http://www.cazy.org/CBM92.html CAZy database], these GH families comprise enzymes with various substrate specificities, including κ-carrageenase ([[GH16]]_17), chitinase ([[GH19]] and [GH18]]), fucosidase ([[GH95]]), β-1,6-glucanase ([[GH30]]), β-1,3-glucanase ([[GH16]]), and galactosidase ([[GH95]]).

To evaluate the feasibility of Cgk16A-CBM92 as a tool in the ''in situ'' investigation of carrageenan, a fluorescent probe was constructed by fusing Cgk16A-CBM92 with a green fluorescent protein. The ''in situ'' visualization of carrageenan in red alga ''Kappaphycus alvarezii'' was realized by utilizing the fluorescent probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified: The first published CBM92 member <cite>Mei2022</cite> is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite>, which was discovered from a marine bacterium ''Wenyingzhuangia aestuarii'' OF219.
;First Structural Characterization: The structures of ''Cp''CBM92A and ''Cp''CBM92B were solved by [[User:Scott Mazurkewich| Scott Mazurkewich]] using X-ray crystallography <cite>Hao2024</cite>. These CBM92 domains flank a [[GH18]] chitinase <cite>Li2023</cite> within a large multi-modular enzyme that also contains a weakly-acting [[GH5]]_46 β-1,6-glucanase <cite>Lu2023</cite>. The modular enzyme is encoded by the genome of ''Chitinophaga pinensis''.

== References ==
<biblio>
#Mei2022 pmid=35830544
#Shen2018 pmid=29355636
#Hao2024 pmid=38653764
#Zhou2017 pmid=28625980
#Lu2023 pmid=36610032
#Li2023 pmid=37121306
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM092]]

Carbohydrate Binding Module Family 92

2024-05-16T10:35:36Z

Lauren McKee:

{{CuratorApproved}}
* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]] and [[User:Lauren McKee|Lauren McKee]]

* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]

----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM92.html
|}
</div>


== Ligand specificities ==
The first published CBM92 domain, and founding member of the CBM92 family, is the Cgk16A-CBM92 from the marine bacterium ''Wenyingzhuangia aestuarii'' OF219 <cite>Mei2022</cite>. The CBM92 bound specifically to the red algal polysaccharide carrageenan, a substrate of the appended [[GH16]] enzyme domain. It was incapable of binding to other polysaccharide components in red algae including agarose, porphyran, and funoran <cite>Mei2022</cite>. Meanwhile, the CBM92 displayed no affinity to several anionic polysaccharides, namely pectin, chondroitin sulfates, dermatan sulfate, and sulfated fucans <cite>Mei2022</cite>. The Cgk16A-CBM92 showed no significant difference in the affinity to κ- and ι-carrageenan.

An earlier paper had demonstrated carbohydrate binding by a so-called Bacterial Fascin-like Domain (BFLD) within the [[GH16]] β−1,3-glucanase LamC from a myxobacterial ''Corallococcus'' species. Affinity gel electrophoresis showed that the domain, now recognized as a [http://www.cazy.org/CBM92.html CBM92 domain] could bind to β−1,3-glucans <cite>Zhou2017</cite>. Later, Lu et al showed binding to β-1,6-glucan by a CBM92 domain found within ''Cp''Glu30A, a [[GH30]] β-1,6-glucanase <cite>Lu2023</cite>. Binding to the Glc- β-1,6-Glc structure found in pustulan, laminarin, scleroglucan, and yeast β-glucan has since been demonstrated for 12 additional members of family CBM92, none of which were able to bind carrageenan <cite>Hao2024</cite>.

== Structural Features ==
[[File:CBM92logo.png|thumb|400px|right|'''Figure 1'''. A consensus sequence logo generated from an alignment of 818 CBM92 domain sequences, including all carrageenan- and β-glucan binders characterised as of May 2024.]]

Several conserved residues (e.g., Phe-70, Arg-72, and Phe-75) were discovered through the multiple sequence alignments of Cgk16A-CBM92 and its close homologs <cite>Mei2022</cite>, which were suggested to be critical for the ligand binding of that CBM. Phylogenetic analysis by Hao et al later showed that the homologs of Cgk16A-CBM92 represent a small sub-group within the CBM92 family (Fig. 1) <cite>Hao2024</cite>. In most other members of CBM92, there are three apparent binding sites identified by a conserved WExF sequence motif. The Trp of this motif is the principal sugar-binding residue, as evidenced by a site-directed mutagenesis study that could abolish binding by altering these residues to Ala <cite>Hao2024</cite>. The same paper also showed that wild-type proteins with fewer Trp-containing binding sites generally showed weaker binding to polysaccharide ligand <cite>Hao2024</cite>. A conserved CNR motif is found just to the N-terminal of the WExF sequence (Fig. 1). Structural analysis revealed that the Arg of this trio contributes to ligand binding, although it is absent in some binding sites in some proteins <cite>Hao2024</cite>.

[[File:CBM92structure.png|thumb|400px|right|'''Figure 2'''. '''a''' Overall structures of (left) ''Cp''CBM92A and (right) ''Cp''CBM92B with their subdomains distinctly coloured and their ligand binding Trp and Glu residues shown as sticks. '''b''' The β-subdomain of ''Cp''CBM92B in complex with glucose. '''c''' Overlay of the ''Cp''CBM92A and -B subdomains showing sequence conservation within all putative binding sites. Single letter residue codes are coloured based on the subdomains shown in panel '''a''' , and are labelled for subdomains ⍺/β/γ, in that order, with the ''Cp''CBM92A codes shown above those for ''Cp''CBM92B. Figure generated by [[User:Scott Mazurkewich| Scott Mazurkewich]] ]]

The crystal structures of ''Cp''CBM92A and ''Cp''CBM92B reveal a β-trefoil structure comprised of 12 β-strands arranged into 3 subdomains (⍺, β, and γ), like the β-trefoil domains found in Fascin and [[CBM13]] proteins (Fig.2). Soaking experiments of ''Cp''CBM92B crystals with glucose, gentiobiose, and sophorose revealed a binding cleft within each subdomain comprising a Trp-Glu binding pair, contributed by the WExF motifs <cite>Hao2024</cite>. Ligand-bound structures suggest the potential for end-on binding to glucose and glucan oligo- or polysaccharides of potentially any linkage, but also reveal the possibility for extensions from both the O1 and O6 positions, enabling the observed mid-chain binding to a β−1,6-glucan such as pustulan, or to β-1,6-linked glucosyl substitutions in scleroglucan or laminarin.

== Functionalities ==
[[File:Figure 1.png|thumb|400px|right|'''Figure 3. Domain architecture of the κ-carrageenase Cgk16A. '''The enzyme consists of a signal peptide (1-20 amino acids), a GH16 domain (21-347 amino acids), a CBM92 domain (viz., Cgk16A-CBM92; 378-490 amino acids) and a C-terminal Sorting domain (516-581 amino acids).''' ]]

In the natural context, Cgk16A-CBM92 is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite> (Fig. 3). It thus might maintain the enzyme near its substrate to improve the enzymatic activity via the proximity effect. The same observation was made for a β-1,6-glucan-binding CBM92 found appended to a [[GH30]] β-1,6-glucanase enzyme from the environmental bacterium ''Chitinophaga pinensis'' <cite>Lu2023</cite>.

Members of the CBM92 family are present in different glycoside hydrolase (GH) family sequences, e.g., [[GH16]]_17, [[GH5]]_46, [[GH5]]_54, [[GH18]], [[GH19]], [[GH30]], and [[GH95]]. According to the [http://www.cazy.org/CBM92.html CAZy database], these GH families comprise enzymes with various substrate specificities, including κ-carrageenase ([[GH16]]_17), chitinase ([[GH19]] and [GH18]]), fucosidase ([[GH95]]), β-1,6-glucanase ([[GH30]]), β-1,3-glucanase ([[GH16]]), and galactosidase ([[GH95]]).

To evaluate the feasibility of Cgk16A-CBM92 as a tool in the ''in situ'' investigation of carrageenan, a fluorescent probe was constructed by fusing Cgk16A-CBM92 with a green fluorescent protein. The ''in situ'' visualization of carrageenan in red alga ''Kappaphycus alvarezii'' was realized by utilizing the fluorescent probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified: The first published CBM92 member <cite>Mei2022</cite> is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite>, which was discovered from a marine bacterium ''Wenyingzhuangia aestuarii'' OF219.
;First Structural Characterization: The structures of ''Cp''CBM92A and ''Cp''CBM92B were solved by [[User:Scott Mazurkewich| Scott Mazurkewich]] using X-ray crystallography <cite>Hao2024</cite>. These CBM92 domains flank a [[GH18]] chitinase <cite>Li2023</cite> within a large multi-modular enzyme that also contains a weakly-acting [[GH5]]_46 β-1,6-glucanase <cite>Lu2023</cite>. The modular enzyme is encoded by the genome of ''Chitinophaga pinensis''.

== References ==
<biblio>
#Mei2022 pmid=35830544
#Shen2018 pmid=29355636
#Hao2024 pmid=38653764
#Zhou2017 pmid=28625980
#Lu2023 pmid=36610032
#Li2023 pmid=37121306
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM092]]

Carbohydrate Binding Module Family 92

2024-05-16T10:32:34Z

Lauren McKee:

{{CuratorApproved}}
* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]] and [[User:Lauren McKee|Lauren McKee]]

* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]

----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM92.html
|}
</div>


== Ligand specificities ==
The first published member in the CBM92 family is the Cgk16A-CBM92 from the marine bacterium ''Wenyingzhuangia aestuarii'' OF219 <cite>Mei2022</cite>. The CBM92 bound specifically to the red algal polysaccharide carrageenan, a substrate of the appended [[GH16]] enzyme domain. It was incapable of binding to other polysaccharide components in red algae including agarose, porphyran, and funoran <cite>Mei2022</cite>. Meanwhile, the CBM92 displayed no affinity to several anionic polysaccharides, namely pectin, chondroitin sulfates, dermatan sulfate, and sulfated fucans <cite>Mei2022</cite>. The Cgk16A-CBM92 showed no significant difference in the affinity to κ- and ι-carrageenan.

An earlier paper had demonstrated carbohydrate binding by a so-called Bacterial Fascin-like Domain (BFLD) within the [[GH16]] β−1,3-glucanase LamC from a myxobacterial ''Corallococcus'' species. Affinity gel electrophoresis showed that the domain, now recognized as a [http://www.cazy.org/CBM92.html CBM92 domain] could bind to β−1,3-glucans <cite>Zhou2017</cite>. Later, Lu et al showed binding to β-1,6-glucan by a CBM92 domain found within ''Cp''Glu30A, a [[GH30]] β-1,6-glucanase <cite>Lu2023</cite>. Binding to the Glc- β-1,6-Glc structure found in pustulan, laminarin, scleroglucan, and yeast β-glucan has since been demonstrated for 12 additional members of family CBM92, none of which were able to bind carrageenan <cite>Hao2024</cite>.

== Structural Features ==
[[File:CBM92logo.png|thumb|400px|right|'''Figure 1'''. A consensus sequence logo generated from an alignment of 818 CBM92 domain sequences, including all carrageenan- and β-glucan binders characterised as of May 2024.]]

Several conserved residues (e.g., Phe-70, Arg-72, and Phe-75) were discovered through the multiple sequence alignments of Cgk16A-CBM92 and its close homologs <cite>Mei2022</cite>, which were suggested to be critical for the ligand binding of that CBM. Phylogenetic analysis by Hao et al later showed that the homologs of Cgk16A-CBM92 represent a small sub-group within the CBM92 family (Fig. 1) <cite>Hao2024</cite>. In most other members of CBM92, there are three apparent binding sites identified by a conserved WExF sequence motif. The Trp of this motif is the principal sugar-binding residue, as evidenced by a site-directed mutagenesis study that could abolish binding by altering these residues to Ala <cite>Hao2024</cite>. The same paper also showed that wild-type proteins with fewer Trp-containing binding sites generally showed weaker binding to polysaccharide ligand <cite>Hao2024</cite>. A conserved CNR motif is found just to the N-terminal of the WExF sequence (Fig. 1). Structural analysis revealed that the Arg of this trio contributes to ligand binding, although it is absent in some binding sites in some proteins <cite>Hao2024</cite>.

[[File:CBM92structure.png|thumb|400px|right|'''Figure 2'''. '''a''' Overall structures of (left) ''Cp''CBM92A and (right) ''Cp''CBM92B with their subdomains distinctly coloured and their ligand binding Trp and Glu residues shown as sticks. '''b''' The β-subdomain of ''Cp''CBM92B in complex with glucose. '''c''' Overlay of the ''Cp''CBM92A and -B subdomains showing sequence conservation within all putative binding sites. Single letter residue codes are coloured based on the subdomains shown in panel '''a''' , and are labelled for subdomains ⍺/β/γ, in that order, with the ''Cp''CBM92A codes shown above those for ''Cp''CBM92B. Figure generated by [[User:Scott Mazurkewich| Scott Mazurkewich]] ]]

The crystal structures of ''Cp''CBM92A and ''Cp''CBM92B reveal a β-trefoil structure comprised of 12 β-strands arranged into 3 subdomains (⍺, β, and γ), like the β-trefoil domains found in Fascin and [[CBM13]] proteins (Fig.2). Soaking experiments of ''Cp''CBM92B crystals with glucose, gentiobiose, and sophorose revealed a binding cleft within each subdomain comprising a Trp-Glu binding pair, contributed by the WExF motifs <cite>Hao2024</cite>. Ligand-bound structures suggest the potential for end-on binding to glucose and glucan oligo- or polysaccharides of potentially any linkage, but also reveal the possibility for extensions from both the O1 and O6 positions, enabling the observed mid-chain binding to a β−1,6-glucan such as pustulan, or to β-1,6-linked glucosyl substitutions in scleroglucan or laminarin.

== Functionalities ==
[[File:Figure 1.png|thumb|400px|right|'''Figure 3. Domain architecture of the κ-carrageenase Cgk16A. '''The enzyme consists of a signal peptide (1-20 amino acids), a GH16 domain (21-347 amino acids), a CBM92 domain (viz., Cgk16A-CBM92; 378-490 amino acids) and a C-terminal Sorting domain (516-581 amino acids).''' ]]

In the natural context, Cgk16A-CBM92 is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite> (Fig. 3). It thus might maintain the enzyme near its substrate to improve the enzymatic activity via the proximity effect. The same observation was made for a β-1,6-glucan-binding CBM92 found appended to a [[GH30]] β-1,6-glucanase enzyme from the environmental bacterium ''Chitinophaga pinensis'' <cite>Lu2023</cite>.

Members of the CBM92 family are present in different glycoside hydrolase (GH) family sequences, e.g., [[GH16]]_17, [[GH5]]_46, [[GH5]]_54, [[GH18]], [[GH19]], [[GH30]], and [[GH95]]. According to the [http://www.cazy.org/CBM92.html CAZy database], these GH families comprise enzymes with various substrate specificities, including κ-carrageenase ([[GH16]]_17), chitinase ([[GH19]] and [GH18]]), fucosidase ([[GH95]]), β-1,6-glucanase ([[GH30]]), β-1,3-glucanase ([[GH16]]), and galactosidase ([[GH95]]).

To evaluate the feasibility of Cgk16A-CBM92 as a tool in the ''in situ'' investigation of carrageenan, a fluorescent probe was constructed by fusing Cgk16A-CBM92 with a green fluorescent protein. The ''in situ'' visualization of carrageenan in red alga ''Kappaphycus alvarezii'' was realized by utilizing the fluorescent probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified: The first published CBM92 member <cite>Mei2022</cite> is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite>, which was discovered from a marine bacterium ''Wenyingzhuangia aestuarii'' OF219.
;First Structural Characterization: The structures of ''Cp''CBM92A and ''Cp''CBM92B were solved by [[User:Scott Mazurkewich| Scott Mazurkewich]] using X-ray crystallography <cite>Hao2024</cite>. These CBM92 domains flank a [[GH18]] chitinase <cite>Li2023</cite> within a large multi-modular enzyme that also contains a weakly-acting [[GH5]]_46 β-1,6-glucanase <cite>Lu2023</cite>. The modular enzyme is encoded by the genome of ''Chitinophaga pinensis''.

== References ==
<biblio>
#Mei2022 pmid=35830544
#Shen2018 pmid=29355636
#Hao2024 pmid=38653764
#Zhou2017 pmid=28625980
#Lu2023 pmid=36610032
#Li2023 pmid=37121306
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM092]]

Carbohydrate Binding Module Family 92

2024-05-16T10:05:12Z

Lauren McKee: Added information about beta-glucan binders including the crystal structures and several additional references.

{{CuratorApproved}}
* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]] and [[User:Lauren McKee|Lauren McKee]]

* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]

----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM92.html
|}
</div>


== Ligand specificities ==
The first published member in the CBM92 family is the Cgk16A-CBM92 from the marine bacterium ''Wenyingzhuangia aestuarii'' OF219 <cite>Mei2022</cite>. The CBM92 bound specifically to the red algal polysaccharide carrageenan, a substrate of the appended [[GH16]] enzyme domain. It was incapable of binding to other polysaccharide components in red algae including agarose, porphyran, and funoran <cite>Mei2022</cite>. Meanwhile, the CBM92 displayed no affinity to several anionic polysaccharides, namely pectin, chondroitin sulfates, dermatan sulfate, and sulfated fucans <cite>Mei2022</cite>. The Cgk16A-CBM92 showed no significant difference in the affinity to κ- and ι-carrageenan.

An earlier paper had demonstrated carbohydrate binding by a so-called Bacterial Fascin-like Domain (BFLD) within the [[GH16]] β−1,3-glucanase LamC from a myxobacterial ''Corallococcus'' species. Affinity gel electrophoresis showed that the domain, now recognized as a [http://www.cazy.org/CBM92.html CBM92 domain] could bind to β−1,3-glucans <cite>Zhou2017</cite>. Later, Lu et al showed binding to β-1,6-glucan by a CBM92 domain found within ''Cp''Glu30A, a [[GH30]] β-1,6-glucanase <cite>Lu2023</cite>. Binding to the Glc- β-1,6-Glc structure found in pustulan, laminarin, scleroglucan, and yeast β-glucan has since been demonstrated for 12 additional members of family CBM92, none of which were able to bind carrageenan <cite>Hao2024</cite>.

== Structural Features ==
[[File:CBM92logo.png|thumb|400px|right|'''Figure 1'''. A consensus sequence logo generated from an alignment of 818 CBM92 domain sequences, including all carrageenan- and β-glucan binders characterised as of May 2024.]]

Several conserved residues (e.g., Phe-70, Arg-72, and Phe-75) were discovered through the multiple sequence alignments of Cgk16A-CBM92 and its close homologs <cite>Mei2022</cite>, which were suggested to be critical for the ligand binding of that CBM. Phylogenetic analysis by Hao et al later showed that the homologs of Cgk16A-CBM92 represent a small sub-group within the CBM92 family (Fig. 1) <cite>Hao2024</cite>. In most other members of CBM92, there are three apparent binding sites identified by a conserved WExF sequence motif. The Trp of this motif is the principal sugar-binding residue, as evidenced by a site-directed mutagenesis study that could abolish binding by altering these residues to Ala <cite>Hao2024</cite>. The same paper also showed that wild-type proteins with fewer Trp-containing binding sites generally showed weaker binding to polysaccharide ligand <cite>Hao2024</cite>. A conserved CNR motif is found just to the N-terminal of the WExF sequence (Fig. 1). Structural analysis revealed that the Arg of this trio contributes to ligand binding, although it is absent in some binding sites in some proteins <cite>Hao2024</cite>.

[[File:CBM92structure.png|thumb|400px|right|'''Figure 2'''. '''a''' Overall structures of (left) ''Cp''CBM92A and (right) ''Cp''CBM92B with their subdomains distinctly coloured and their ligand binding Trp and Glu residues shown as sticks. '''b''' The β-subdomain of ''Cp''CBM92B in complex with glucose. '''c''' Overlay of the ''Cp''CBM92A and -B subdomains showing sequence conservation within all putative binding sites. Single letter residue codes are coloured based on the subdomains shown in panel '''a''' , and are labelled for subdomains ⍺/β/γ, in that order, with the ''Cp''CBM92A codes shown above those for ''Cp''CBM92B. Figure generated by [[User:Scott Mazurkewich| Scott Mazurkewich]] ]]

The crystal structures of ''Cp''CBM92A and ''Cp''CBM92B reveal a β-trefoil structure comprised of 12 β-strands arranged into 3 subdomains (⍺, β, and γ), like the β-trefoil domains found in Fascin and [[CBM13]] proteins (Fig.2). Soaking experiments of ''Cp''CBM92B crystals with glucose, gentiobiose, and sophorose revealed a binding cleft within each subdomain comprising a Trp-Glu binding pair, contributed by the WExF motifs <cite>Hao2024</cite>. Ligand-bound structures suggest the potential for end-on binding to glucose and glucan oligo- or polysaccharides of potentially any linkage, but also reveal the possibility for extensions from both the O1 and O6 positions, enabling the observed mid-chain binding to a β−1,6-glucan such as pustulan, or to β-1,6-linked glucosyl substitutions in scleroglucan or laminarin.

== Functionalities ==
[[File:Figure 1.png|thumb|400px|right|'''Figure 3. Domain architecture of the κ-carrageenase Cgk16A. '''The enzyme consists of a signal peptide (1-20 amino acids), a GH16 domain (21-347 amino acids), a CBM92 domain (viz., Cgk16A-CBM92; 378-490 amino acids) and a C-terminal Sorting domain (516-581 amino acids).''' ]]

In the natural context, Cgk16A-CBM92 is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite> (Fig. 3). It thus might maintain the enzyme near its substrate to improve the enzymatic activity via the proximity effect. The same observation was made for a β-1,6-glucan-binding CBM92 found appended to a [[GH30]] β-1,6-glucanase enzyme from the environmental bacterium “Chitinophaga pinensis" <cite>Lu2023</cite>.

Members of the CBM92 family are present in different glycoside hydrolase (GH) family sequences, e.g., [[GH16]]_17, [[GH5]]_46, [[GH5]]_54, [[GH18]], [[GH19]], [[GH30]], and [[GH95]]. According to the [http://www.cazy.org/CBM92.html CAZy database], these GH families comprise enzymes with various substrate specificities, including κ-carrageenase ([[GH16]]_17), chitinase ([[GH19]] and [GH18]]), fucosidase ([[GH95]]), β-1,6-glucanase ([[GH30]]), β-1,3-glucanase ([[GH16]]), and galactosidase ([[GH95]]).

To evaluate the feasibility of Cgk16A-CBM92 as a tool in the ''in situ'' investigation of carrageenan, a fluorescent probe was constructed by fusing Cgk16A-CBM92 with a green fluorescent protein. The ''in situ'' visualization of carrageenan in red alga ''Kappaphycus alvarezii'' was realized by utilizing the fluorescent probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified: The first published CBM92 member <cite>Mei2022</cite> is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite>, which was discovered from a marine bacterium ''Wenyingzhuangia aestuarii'' OF219.
;First Structural Characterization: The structures of ''Cp''CBM92A and ''Cp''CBM92B were solved by [[User:Scott Mazurkewich| Scott Mazurkewich]] using X-ray crystallography <cite>Hao2024</cite>. These CBM92 domains flank a [[GH18]] chitinase <cite>Li2023</cite> within a large multi-modular enzyme that also contains a weakly-acting [[GH5]]_46 β-1,6-glucanase <cite>Lu2023</cite>. The modular enzyme is encoded by the genome of “Chitinophaga pinensis".

== References ==
<biblio>
#Mei2022 pmid=35830544
#Shen2018 pmid=29355636
#Hao2024 pmid=38653764
#Zhou2017 pmid=28625980
#Lu2023 pmid=36610032
#Li2023 pmid=37121306
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM092]]

Carbohydrate Binding Module Family 92

2024-05-16T10:02:09Z

Lauren McKee:

{{CuratorApproved}}
* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]] and [[User:Lauren McKee|Lauren McKee]]

* [[Responsible Curator]]: [[User:Yaoguang Chang|Yaoguang Chang]]

----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM92.html
|}
</div>


== Ligand specificities ==
The first published member in the CBM92 family is the Cgk16A-CBM92 from the marine bacterium ''Wenyingzhuangia aestuarii'' OF219 <cite>Mei2022</cite>. The CBM92 bound specifically to the red algal polysaccharide carrageenan, a substrate of the appended [[GH16]] enzyme domain. It was incapable of binding to other polysaccharide components in red algae including agarose, porphyran, and funoran <cite>Mei2022</cite>. Meanwhile, the CBM92 displayed no affinity to several anionic polysaccharides, namely pectin, chondroitin sulfates, dermatan sulfate, and sulfated fucans <cite>Mei2022</cite>. The Cgk16A-CBM92 showed no significant difference in the affinity to κ- and ι-carrageenan.

An earlier paper had demonstrated carbohydrate binding by a so-called Bacterial Fascin-like Domain (BFLD) within the [[GH16]] β−1,3-glucanase LamC from a myxobacterial ''Corallococcus'' species. Affinity gel electrophoresis showed that the domain, now recognized as a [http://www.cazy.org/CBM92.html CBM92 domain] could bind to β−1,3-glucans <cite>Zhou2017</cite>. Later, Lu et al showed binding to β-1,6-glucan by a CBM92 domain found within ''Cp''Glu30A, a [[GH30]] β-1,6-glucanase <cite>Lu2023</cite>. Binding to the Glc- β-1,6-Glc structure found in pustulan, laminarin, scleroglucan, and yeast β-glucan has since been demonstrated for 12 additional members of family CBM92, none of which were able to bind carrageenan <cite>Hao2024</cite>.

== Structural Features ==
[[File:CBM92logo.png|thumb|400px|right|'''Figure 1'''. A consensus sequence logo generated from an alignment of 818 CBM92 domain sequences, including all carrageenan- and β-glucan binders characterised as of May 2024.]]

Several conserved residues (e.g., Phe-70, Arg-72, and Phe-75) were discovered through the multiple sequence alignments of Cgk16A-CBM92 and its close homologs <cite>Mei2022</cite>, which were suggested to be critical for the ligand binding of that CBM. Phylogenetic analysis by Hao et al later showed that the homologs of Cgk16A-CBM92 represent a small sub-group within the CBM92 family (Fig. 1) <cite>Hao2024</cite>. In most other members of CBM92, there are three apparent binding sites identified by a conserved WExF sequence motif. The Trp of this motif is the principal sugar-binding residue, as evidenced by a site-directed mutagenesis study that could abolish binding by altering these residues to Ala <cite>Hao2024</cite>. The same paper also showed that wild-type proteins with fewer Trp-containing binding sites generally showed weaker binding to polysaccharide ligand <cite>Hao2024</cite>. A conserved CNR motif is found just to the N-terminal of the WExF sequence (Fig. 1). Structural analysis revealed that the Arg of this trio contributes to ligand binding, although it is absent in some binding sites in some proteins <cite>Hao2024</cite>.

[[File:CBM92structure.png|thumb|400px|right|'''Figure 2'''. '''a''' Overall structures of (left) ''Cp''CBM92A and (right) ''Cp''CBM92B with their subdomains distinctly coloured and their ligand binding Trp and Glu residues shown as sticks. '''b''' The β-subdomain of ''Cp''CBM92B in complex with glucose. '''c''' Overlay of the ''Cp''CBM92A and -B subdomains showing sequence conservation within all putative binding sites. Single letter residue codes are coloured based on the subdomains shown in panel '''a''' , and are labelled for subdomains ⍺/β/γ, in that order, with the ''Cp''CBM92A codes shown above those for ''Cp''CBM92B. Figure generated by [[User:Scott Mazurkewich| Scott Mazurkewich]] ]]

The crystal structures of ''Cp''CBM92A and ''Cp''CBM92B reveal a β-trefoil structure comprised of 12 β-strands arranged into 3 subdomains (⍺, β, and γ), like the β-trefoil domains found in Fascin and [[CBM13]] proteins (Fig.2). Soaking experiments of ''Cp''CBM92B crystals with glucose, gentiobiose, and sophorose revealed a binding cleft within each subdomain comprising a Trp-Glu binding pair, contributed by the WExF motifs <cite>Hao2024</cite>. Ligand-bound structures suggest the potential for end-on binding to glucose and glucan oligo- or polysaccharides of potentially any linkage, but also reveal the possibility for extensions from both the O1 and O6 positions, enabling the observed mid-chain binding to a β−1,6-glucan such as pustulan, or to β-1,6-linked glucosyl substitutions in scleroglucan or laminarin.

== Functionalities ==
[[File:Figure 1.png|thumb|300px|right|'''Figure 3. Domain architecture of the κ-carrageenase Cgk16A. '''The enzyme consists of a signal peptide (1-20 amino acids), a GH16 domain (21-347 amino acids), a CBM92 domain (viz., Cgk16A-CBM92; 378-490 amino acids) and a C-terminal Sorting domain (516-581 amino acids).''' ]]

In the natural context, Cgk16A-CBM92 is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite> (Fig. 3). It thus might maintain the enzyme near its substrate to improve the enzymatic activity via the proximity effect. The same observation was made for a β-1,6-glucan-binding CBM92 found appended to a [[GH30]] β-1,6-glucanase enzyme from the environmental bacterium “Chitinophaga pinensis" <cite>Lu2023</cite>.

Members of the CBM92 family are present in different glycoside hydrolase (GH) family sequences, e.g., [[GH16]]_17, [[GH5]]_46, [[GH5]]_54, [[GH18]], [[GH19]], [[GH30]], and [[GH95]]. According to the [http://www.cazy.org/CBM92.html CAZy database], these GH families comprise enzymes with various substrate specificities, including κ-carrageenase ([[GH16]]_17), chitinase ([[GH19]] and [GH18]]), fucosidase ([[GH95]]), β-1,6-glucanase ([[GH30]]), β-1,3-glucanase ([[GH16]]), and galactosidase ([[GH95]]).

To evaluate the feasibility of Cgk16A-CBM92 as a tool in the ''in situ'' investigation of carrageenan, a fluorescent probe was constructed by fusing Cgk16A-CBM92 with a green fluorescent protein. The ''in situ'' visualization of carrageenan in red alga ''Kappaphycus alvarezii'' was realized by utilizing the fluorescent probe <cite>Mei2022</cite>.

== Family Firsts ==
;First Identified: The first published CBM92 member <cite>Mei2022</cite> is a component of the κ-carrageenase Cgk16A <cite>Shen2018</cite>, which was discovered from a marine bacterium ''Wenyingzhuangia aestuarii'' OF219.
;First Structural Characterization: The structures of ''Cp''CBM92A and ''Cp''CBM92B were solved by [[User:Scott Mazurkewich| Scott Mazurkewich]] using X-ray crystallography <cite>Hao2024</cite>. These CBM92 domains flank a [[GH18]] chitinase <cite>Li2023</cite> within a large multi-modular enzyme that also contains a weakly-acting [[GH5]]_46 β-1,6-glucanase <cite>Lu2023</cite>. The modular enzyme is encoded by the genome of “Chitinophaga pinensis".

== References ==
<biblio>
#Mei2022 pmid=35830544
#Shen2018 pmid=29355636
#Hao2024 pmid=38653764
#Zhou2017 pmid=28625980
#Lu2023 pmid=36610032
#Li2023 pmid=37121306
</biblio>


[[Category:Carbohydrate Binding Module Families|CBM092]]

File:CBM92structure.png

2024-05-16T09:33:12Z

Lauren McKee: Three dimensional structures of two CBM92 domains.

== Summary ==
Three dimensional structures of two CBM92 domains.

File:CBM92logo.png

2024-05-16T09:32:39Z

Lauren McKee: Consensus logo sequence for CBM family 92 domains.

== Summary ==
Consensus logo sequence for CBM family 92 domains.

User:Lauren McKee

2024-05-14T14:34:58Z

Lauren McKee:

[[Image:LaurenMcKee.jpeg|200px|right]]
I hold the position of Researcher with Docent (Reader/Associate Prof-equivalent) in Biotechnology at the [https://www.kth.se/che/glykovetenskap/division-of-glycoscience-1.785898 KTH Division of Glycoscience] in Stockholm, Sweden. I am principal investigator for the [https://stockholmcazyme.com/ Stockholm CAZyme group]. And, since January 2023, I am a vice-director for a national [https://wwsc.se/wwsc-academy/ PhD Academy] in Sweden, financed by the [https://wwsc.se/ Wallenberg Wood Science Centre] network.
I studied for my Biochemistry BSc, Environmental Biogeochemistry MSc, and Carbohydrate Enzymology PhD in my home town, at Newcastle University, UK. My doctoral research focussed on structure-function analysis of [[GH43]] enzymes <cite>Cartmell2011</cite> <cite>McKee2012</cite> and was supervised by Professor [[User:Harry Gilbert|Harry Gilbert]]. I spent almost two years with Harry at the [https://ccrc.uga.edu/ Complex Carbohydrate Research Centre] at UGA, Georgia, USA. Shortly after completing my PhD, I moved to Stockholm to begin a post-doctoral scholarship position supervised by Professor [[User:Harry Brumer|Harry Brumer]] <cite>Larsbrink2014</cite> <cite>McKee2015</cite>, before he moved to UBC in Canada. When Harry moved, I worked with Prof Vincent Bulone <cite>McKee2016</cite> <cite>Larsbrink2017</cite> until I secured my own independent funding and could begin to run my own team and projects.
My main interests are the discovery and characterisation of glycoside hydrolases, glycosyltransferases, polysaccharide utilisation loci <cite>McKee2021</cite> <cite>Lu2023b</cite>, and carbohydrate binding modules (especially family [[CBM92]] <cite>Hao2024</cite>), with a particular focus on environmental bacteria from soil, marine, and industrial ecosystems <cite>McKee2019</cite> <cite>Lu2023a</cite>.

----

<biblio>
#Hao2024 pmid=38653764
#Lu2023a pmid=37493618
#Lu2023b pmid=36610032
#McKee2021 pmid=34036727
#McKee2019 pmid=30413479
#Larsbrink2017 pmid=28069559
#McKee2016 pmid=26734072
#McKee2015 pmid=26448175
#Larsbrink2014 pmid=24463512
#McKee2012 pmid=22492980
#Cartmell2011 pmid=21339299

</biblio>


[[Category:Contributors|McKee,Lauren]]

User:Lauren McKee

2024-05-14T13:29:15Z

Lauren McKee:

[[Image:LaurenMcKee.jpeg|200px|right]]
I hold the position of Researcher with Docent in Biotechnology at the [https://www.kth.se/che/glykovetenskap/division-of-glycoscience-1.785898 KTH Division of Glycoscience] in Stockholm, Sweden. I am principal investigator for the [https://stockholmcazyme.com/ Stockholm CAZyme group]. And, since January 2023, I am a vice-director for a national [https://wwsc.se/wwsc-academy/ PhD Academy] in Sweden, financed by the [https://wwsc.se/ Wallenberg Wood Science Centre] network.
I studied for my Biochemistry BSc, Environmental Biogeochemistry MSc, and Carbohydrate Enzymology PhD in my home town, at Newcastle University, UK. My doctoral research focussed on structure-function analysis of [[GH43]] enzymes <cite>Cartmell2011</cite> <cite>McKee2012</cite> and was supervised by Professor [[User:Harry Gilbert|Harry Gilbert]]. I spent almost two years with Harry at the [https://ccrc.uga.edu/ Complex Carbohydrate Research Centre] at UGA, Georgia, USA. Shortly after completing my PhD, I moved to Stockholm to begin a post-doctoral scholarship position supervised by Professor [[User:Harry Brumer|Harry Brumer]] <cite>Larsbrink2014</cite> <cite>McKee2015</cite>, before he moved to UBC in Canada. When Harry moved, I worked with Prof Vincent Bulone <cite>McKee2016</cite> <cite>Larsbrink2017</cite> until I secured my own independent funding and could begin to run my own team and projects.
My main interests are the discovery and characterisation of glycoside hydrolases, glycosyltransferases, polysaccharide utilisation loci <cite>McKee2021</cite> <cite>Lu2023b</cite>, and carbohydrate binding modules (especially family [[CBM92]] <cite>Hao2024</cite>), with a particular focus on environmental bacteria from soil, marine, and industrial ecosystems <cite>McKee2019</cite> <cite>Lu2023a</cite>.

----

<biblio>
#Hao2024 pmid=38653764
#Lu2023a pmid=37493618
#Lu2023b pmid=36610032
#McKee2021 pmid=34036727
#McKee2019 pmid=30413479
#Larsbrink2017 pmid=28069559
#McKee2016 pmid=26734072
#McKee2015 pmid=26448175
#Larsbrink2014 pmid=24463512
#McKee2012 pmid=22492980
#Cartmell2011 pmid=21339299

</biblio>


[[Category:Contributors|McKee,Lauren]]

User:Lauren McKee

2024-05-14T13:04:53Z

Lauren McKee:

[[Image:LaurenMcKee.jpeg|200px|right]]
'''This is an empty template to help you get started with composing your User page.'''

You should begin by opening this page for editing by clicking on the Edit tab above. Your biography goes in this area of the page.

* See [[User:Gerlind_Sulzenbacher]] for an example. You may copy text from this example by opening the page in another browser window and clicking the "Edit" tab.
* Add your publications in the list below using PubMed IDs and cite them in the text like this <cite>Gilbert2008</cite>.
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----

<biblio>
#Gilbert2008 pmid=18430603

</biblio>


[[Category:Contributors|McKee,Lauren]]

File:LaurenMcKee.jpeg

2024-05-14T13:04:00Z

Lauren McKee: Photo of Lauren McKee taken in 2023 in the AlbaNova building, KTH in Stockholm, Sweden.

== Summary ==
Photo of Lauren McKee taken in 2023 in the AlbaNova building, KTH in Stockholm, Sweden.