Difference between revisions of "Carbohydrate Binding Module Family 105"

Latest revision as of 20:33, 6 November 2024

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

Ligand specificities

The first member of family CBM105 (SoCBM105) was identified in the PL29 multidomain chondroitinase SoChABC29 from Segatella oris [1]. SoCBM105 bound specifically to chondroitin sulfates (CSs) including CS-A and CS-C, while it was incapable of binding to other glycosaminoglycans or polyuronic acid substrates [1].

Structural Features

Figure 1. Domain analysis of SoChABC29, the parent enzyme of SoCBM105 [2]. The enzyme consists of a signal peptide (1-21 amino acids), a PL29 domain (66-380 amino acids) and a CBM105 domain (viz., SoCBM105; 555-785 amino acids).

An AlphaFold2 [2] model predicts that SoCBM105 has a β-sandwich fold (Fig.1).

Functionalities

SoCBM105 is at the C-terminus domain of a PL29 enzyme SoChABC29 that displays chondroitin sulfate ABC activity, consistent with the SoCBM105 specificity [1]. Biochemical characterization of SoChABC29 and the CBM-truncated enzyme revealed that the SoCBM105 enhances the catalytic activity, thermostability, and disaccharide proportion in the final enzymatic products of SoChABC29 [1].

Family Firsts

First Identified: Binding to chondroitin sulfate in the CBM105 family was first characterized and identified for SoCBM105 from the S. oris PL29 chondroitinase [1].
First Structural Characterization: No experimentally determined three-dimensional structure has been solved in this CBM family.

References

All Medline abstracts: PubMed

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]: [[User:Guanchen Liu|Guanchen Liu]]
 * [[Responsible Curator]]:  [[User:Yaoguang Chang|Yaoguang Chang]]
@@ 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 (SoCBM105) was identified in the [[PL29]] multidomain chondroitinase SoChABC29 from ''Segatella oris'' <cite>Liu2024</cite>. SoCBM105 bound specifically to chondroitin sulfates (CSs) including CS-A and CS-C, while it was incapable of binding to other glycosaminoglycans or polyuronic acid substrates <cite>Liu2024</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:CBM105 Fig.1.png|thumb|350px|right|'''Figure 1. Domain analysis of SoChABC29, the parent enzyme of SoCBM105 <cite>Jumper2021</cite>.''' The enzyme consists of a signal peptide (1-21 amino acids), a PL29 domain (66-380 amino acids) and a CBM105 domain (viz., SoCBM105; 555-785 amino acids).]]
-* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
+An AlphaFold2 <cite>Jumper2021</cite> model predicts that SoCBM105 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:''
+SoCBM105 is at the C-terminus domain of a [[PL29]] enzyme SoChABC29 that displays chondroitin sulfate ABC activity, consistent with the SoCBM105 specificity <cite>Liu2024</cite>. Biochemical characterization of SoChABC29 and the CBM-truncated enzyme revealed that the SoCBM105 enhances the catalytic activity, thermostability, and disaccharide proportion in the final enzymatic products of SoChABC29 <cite>Liu2024</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: Binding to chondroitin sulfate in the CBM105 family was first characterized and identified for SoCBM105 from the ''S. oris'' [[PL29]] chondroitinase <cite>Liu2024</cite>.
-:Insert archetype here, possibly including ''very brief'' synopsis.
+;First Structural Characterization: No experimentally determined three-dimensional structure has been solved in this CBM family.
-;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
 == 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].
+#Jumper2021 pmid=34265844
-#Boraston2004 pmid=15214846
-#Hashimoto2006 pmid=17131061
-#Shoseyov2006 pmid=16760304
-#Guillen2010 pmid=19908036
-#Armenta2017 pmid=28547780
 </biblio>