Difference between revisions of "Carbohydrate Binding Module Family 105"

Revision as of 19:09, 27 October 2024

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CAZy DB link
https://www.cazy.org/CBM105.html

Ligand specificities

The first member of family CBM105 (SoCBM) was identified in the PL29 multidomain chondroitinase ChABC29So from Segatella oris [1]. SoCBM bound specifically to chondroitin sulfates (CSs) including CS-A and CS-C, while incapable of binding to other glycosaminoglycanss or polyuronic acid substrates.

Structural Features

Figure 1. Domain analysis of ChABC29So, the parent enzyme of SoCBM.The enzyme consists of a signal peptide (1-21 amino acids), a PL29 domain (66-380 amino acids) and a CBM105 domain (viz., SoCBM; 555-785 amino acids).

An AlphaFold2 model predicts that SoCBM has a β-sandwich fold (Fig.1).

Functionalities

SoCBM is the C-terminus domain of a PL29 enzyme ChABC29So that displays chondroitin sulfate ABC activity, consistent with the SoCBM specificity. Biochemical characterization of ChABC29So and the CBM-truncated enzyme revealed that the SoCBM enhances the catalytic activity, thermostability, and disaccharide proportion in the final enzymatic products of ChABC29So.

Family Firsts

First Identified: The chondroitin sulfate binding SoCBM from the S. oris PL29 chondroitinase was the first member of the family to be identified and characterized[1].
First Structural Characterization: No experimentally determined three-dimensional structure has been solved in this CBM family.

References

Liu G, Song L, Li J, Song X, Mei X, Zhang Y, Fan C, Chang Y, and Xue C. (2024). Identification and characterization of a chondroitinase ABC with a novel carbohydrate-binding module. Int J Biol Macromol. 2024;271(Pt 1):132518. DOI:10.1016/j.ijbiomac.2024.132518 | PubMed ID:38777025 [Liu2024]

@@ 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.
+The first member of family CBM105 (SoCBM) was identified in the [[PL29]] multidomain chondroitinase ChABC29So from ''Segatella oris'' <cite>Liu2024</cite>. SoCBM bound specifically to chondroitin sulfates (CSs) including CS-A and CS-C, while incapable of binding to other glycosaminoglycanss or polyuronic acid substrates.
-''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:CBM105 Fig.1.png|thumb|350px|right|'''Figure 1. Domain analysis of ChABC29So, the parent enzyme of SoCBM.'''The enzyme consists of a signal peptide (1-21 amino acids), a PL29 domain (66-380 amino acids) and a CBM105 domain (viz., SoCBM; 555-785 amino acids).]]
-* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
+An AlphaFold2 model predicts that SoCBM has a β-sandwich fold (Fig.1).
-* '''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:''
+SoCBM is the C-terminus domain of a [[PL29]] enzyme ChABC29So that displays chondroitin sulfate ABC activity, consistent with the SoCBM specificity. Biochemical characterization of ChABC29So and the CBM-truncated enzyme revealed that the SoCBM enhances the catalytic activity, thermostability, and disaccharide proportion in the final enzymatic products of ChABC29So.
-* '''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 chondroitin sulfate binding SoCBM from the ''S. oris'' [[PL29]] chondroitinase was the first member of the family to be identified and characterized<cite>Liu2024</cite>.
 ;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
+:No experimentally determined three-dimensional structure has been solved in this CBM family.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Liu2024 pmid=38777025
-#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>