Difference between revisions of "Carbohydrate Binding Module Family 106"

Revision as of 02:48, 30 October 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 found in the marine bacteria Vibrio breoganii. 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 [1].

Structural Features

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. Site-directed mutagenesis assays demonstrated that the residues R59, R61, K63, K139, and R190 play critical roles in the ligand binding of VbCBM106 [1].

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 could enhance the catalytic efficiency of its appended enzymes by increasing the contact between adjacent catalytic domains and alginate [1].

Family Firsts

First Identified: The first member VbCBM106 is a component of a potential PL6 alginate lyase from a marine bacterium Vibrio breoganii [1].
First Structural Characterization: VbCBM106 (PDB 8zqf) is the first and currently only member of the CBM106 family with the structural information [1].

References

Mei X, Tao W, Sun H, Liu G, Chen G, Zhang Y, Xue C, and Chang Y. (2024). Characterization and structural identification of a novel alginate-specific carbohydrate-binding module (CBM): The founding member of a new CBM family. Int J Biol Macromol. 2024;277(Pt 3):134221. DOI:10.1016/j.ijbiomac.2024.134221 | PubMed ID:39069041 [Mei2024]

@@ Line 18: / Line 18: @@
 == 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 found in the marine bacteria ''Vibrio breoganii''. 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:''
+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. 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>.
-* '''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:''
+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 could enhance the catalytic efficiency of its appended enzymes by increasing the contact between adjacent catalytic domains and alginate <cite>Mei2024</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
-:Insert archetype here, possibly including ''very brief'' synopsis.
+:The first member VbCBM106 is a component of a potential [[PL6]] alginate lyase from a marine bacterium ''Vibrio breoganii'' <cite>Mei2024</cite>.
 ;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
+:VbCBM106 ([{{PDBlink}}8zqf PDB 8zqf]) is the first and currently only member of the CBM106 family with the structural information <cite>Mei2024</cite>.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Mei2024 pmid=39069041
-#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].
-#Boraston2004 pmid=15214846
-#Hashimoto2006 pmid=17131061
-#Shoseyov2006 pmid=16760304
-#Guillen2010 pmid=19908036
-#Armenta2017 pmid=28547780
 </biblio>