Carbohydrate Binding Module Family 92 - Revision history

Harry Brumer: /* Family Firsts */ Edited for brevity

2024-05-22T16:07:31Z

Family Firsts: Edited for brevity

Harry Brumer: fixed broken link

2024-05-22T16:04:58Z

fixed broken link

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

2024-05-16T12:42:23Z

Fixed an error in the legend to figure 2.

Lauren McKee at 10:35, 16 May 2024

2024-05-16T10:35:36Z

Lauren McKee at 10:32, 16 May 2024

2024-05-16T10:32:34Z

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

2024-05-16T10:05:12Z

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

Lauren McKee at 10:02, 16 May 2024

2024-05-16T10:02:09Z

Harry Brumer at 13:07, 5 May 2024

2024-05-05T13:07:07Z

Elizabeth Ficko-Blean at 15:34, 2 May 2024

2024-05-02T15:34:45Z

Elizabeth Ficko-Blean: /* Ligand specificities */

2023-04-17T14:21:22Z

Ligand specificities

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 == 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''.
+;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 from ''Chitinophaga pinensis'' that also contains a weakly-acting [[GH5]]_46 β-1,6-glucanase <cite>Lu2023</cite>.
 == References ==

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 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]]).
+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>.

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 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]] ]]
+[[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.

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 == 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.
+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>.

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 [[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>.
+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]]).
@@ Line 43: / Line 43: @@
 == 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".
+;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 ==

@@ Line 33: / Line 33: @@
 == 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).''' ]]
+[[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>.

@@ Line 19: / Line 19: @@
 == Ligand specificities ==
-The first characterized member in the CBM92 family is the Cgk16A-CBM92 from a marine bacterium ''Wenyingzhuangia aestuarii'' OF219 <cite>Mei2022</cite>. The CBM92 bound specifically to the red algal polysaccharide carrageenan. 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.
+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.
 == Structural Features ==
-No three-dimensional structure has been solved in this CBM family at present. 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 might be critical for the ligand binding of this CBM.
+[[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.]]
 == Functionalities ==
-[[File:Figure 1.png|thumb|300px|right|'''Figure 1. 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).''' ]]
+[[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. 1). It thus might maintain the enzyme near its substrate to improve the enzymatic activity via the proximity effect. 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>.
+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]]).
-Members of the CBM92 family are present in different glycoside hydrolase (GH) family sequences, e.g., [[GH16]]_17, [[GH5]]_54, [[GH19]], 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]]), fucosidase ([[GH95]]), and galactosidase ([[GH95]]). It indicated that functional diversity might be present within the CBM92 family.
+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 characterized 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 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: No three-dimensional structure has been solved in this CBM family at present.
+;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 ==
@@ Line 39: / Line 49: @@
 #Mei2022 pmid=35830544
 #Shen2018 pmid=29355636
 </biblio>
 <!-- Do not delete this Category tag -->
 [[Category:Carbohydrate Binding Module Families|CBM092]]

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]] and [[Lauren McKee]]
+* [[Author]]: [[User:Xuanwei Mei|Xuanwei Mei]] and [[User:Lauren McKee|Lauren McKee]]
 * [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]