Difference between revisions of "Carbohydrate Binding Module Family 106"

Latest revision as of 22:06, 20 November 2024

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CAZy DB link
https://www.cazy.org/CBM106.html

Ligand specificities

VbCBM106 represents the first characterized member of the CBM106 family, which is appended to a PL6 potential alginate lyase (GenBank: ANO33061.1) from the marine bacterium Vibrio breoganii [1]. The CBM showed the favorable specificity to alginate, while it could not bind to other polyuronic acids, such as hyaluronic acid, chondroitin sulfates, dermatan sulfate, and pectin, as well as other polysaccharides from brown algae including laminarin and fucoidan [2].

Structural Features

Figure 1. Crystal structure of VbCBM106 (PDB 8zqf). The strand, helix, and loop were colored in cyan, yellow, and white respectively. The sequential order of these strands and helices was depicted from P4 through to G200.

Figure 2. Detailed view of the predicted binding site of VbCBM106. The potential critical residues and their side chains are shown.

The crystal structure (1.55 Å) of VbCBM106 exhibits a typical β-sandwich fold, which is composed of two antiparallel β-sheets formed by 11 β-strands and 4 helixes (Fig.1). Several conserved residues were identified, including S47, S57, R59, R61, F62, K63, Y95, K100, K139, F142, K143, R190, and D192. The conserved residues are spatially adjacent, situated on the concave of one β-sheet and the apical loop region (Fig.2). Site-directed mutagenesis assays demonstrated that the residues R59, R61, K63, K139, and R190 play critical roles in the ligand binding of VbCBM106 [2]. Since VbCBM106 is capable of binding to soluble alginate polysaccharides, it is suggested that it belongs to type B [3].

Functionalities

VbCBM106 and some of its homologous sequences are linked to the catalytic modules of the PL6 family or its subfamily PL6_1. In the natural environments, VbCBM106 might enhance the catalytic efficiency of its appended enzymes by increasing the contact between adjacent catalytic domain and alginate, similar to the role of the CBM13 domain in alginate lyase [4].

Family Firsts

First Identified: The first member VbCBM106 is a component of a potential PL6 alginate lyase from a marine bacterium Vibrio breoganii [2].
First Structural Characterization: VbCBM106 (PDB 8zqf) is the first and currently only member of the CBM106 family with the structural information [2].

References

All Medline abstracts: PubMed

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 * [[Author]]: [[User:Wenwen Tao|Wenwen Tao]]
 * [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]
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 == Ligand specificities ==
-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.
+VbCBM106 represents the first characterized member of the CBM106 family, which is appended to a [[PL6]] potential alginate lyase (GenBank: ANO33061.1) from the marine bacterium ''Vibrio breoganii'' <cite>Hidalgo2009</cite>. The CBM showed the favorable specificity to alginate, while it could not bind to other polyuronic acids, such as hyaluronic acid, chondroitin sulfates, dermatan sulfate, and pectin, as well as other polysaccharides from brown algae including laminarin and fucoidan <cite>Mei2024</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:''
+[[File:CBM106_Fig.1.png|thumb|250px|right|'''Figure 1. Crystal structure of VbCBM106 ([{{PDBlink}}8zqf PDB 8zqf]).''' The strand, helix, and loop were colored in cyan, yellow, and white respectively. The sequential order of these strands and helices was depicted from P4 through to G200.]]
-* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
+[[File:CBM106_Fig.2.png|thumb|250px|right|'''Figure 2. Detailed view of the predicted binding site of VbCBM106.''' The potential critical residues and their side chains are shown.]]
-* '''Type:''' Include here Type A, B, or C and properties
+The crystal structure (1.55 Å) of VbCBM106 exhibits a typical β-sandwich fold, which is composed of two antiparallel β-sheets formed by 11 β-strands and 4 helixes (Fig.1). Several conserved residues were identified, including S47, S57, R59, R61, F62, K63, Y95, K100, K139, F142, K143, R190, and D192. The conserved residues are spatially adjacent, situated on the concave of one β-sheet and the apical loop region (Fig.2). Site-directed mutagenesis assays demonstrated that the residues R59, R61, K63, K139, and R190 play critical roles in the ligand binding of VbCBM106 <cite>Mei2024</cite>.
-* '''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.
+Since VbCBM106 is capable of binding to soluble alginate polysaccharides, it is suggested that it belongs to type B <cite>Boraston2004</cite>.
 == Functionalities ==
-''Content in this section should include, in paragraph form, a description of:''
+VbCBM106 and some of its homologous sequences are linked to the catalytic modules of the PL6 family or its subfamily PL6_1. In the natural environments, VbCBM106 might enhance the catalytic efficiency of its appended enzymes by increasing the contact between adjacent catalytic domain and alginate, similar to the role of the CBM13 domain in alginate lyase <cite>Li2015</cite>.
-* '''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
+;First Identified: The first member VbCBM106 is a component of a potential [[PL6]] alginate lyase from a marine bacterium ''Vibrio breoganii'' <cite>Mei2024</cite>.
-:Insert archetype here, possibly including ''very brief'' synopsis.
+;First Structural Characterization: VbCBM106 ([{{PDBlink}}8zqf PDB 8zqf]) is the first and currently only member of the CBM106 family with the structural information <cite>Mei2024</cite>.
-;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Hidalgo2009 pmid=19542146
-#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. [https://doi.org/10.1042/BIO03004026 DOI:10.1042/BIO03004026].
+#Mei2024 pmid=39069041
 #Boraston2004 pmid=15214846
-#Hashimoto2006 pmid=17131061
+#Li2015 pmid=25837818
-#Shoseyov2006 pmid=16760304
-#Guillen2010 pmid=19908036
-#Armenta2017 pmid=28547780
 </biblio>