Difference between revisions of "Carbohydrate Binding Module Family 75"

Latest revision as of 13:20, 18 December 2021

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CAZy DB link
https://www.cazy.org/CBM75.html

Ligand specificities

CBM75 is a small bacterial family containing only 3 members comprising around 290 amino acids and found exclusively in Ruminococci. The only family member characterized is CBM75_RfGH43 from Ruminococcus flavefaciens that specifically binds to xyloglucan [1]. By isothermal titration calorimetry, the affinity to xyloglucan repeating unit XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) is similar to the polysaccharide, suggesting that CBM75_RfGH43 has four binding sites that recognize the backbone glucose units. However, the specific binding to xyloglucan and not to other β-glucan polysaccharides indicates that at least some of the xylose side chains also have a major contribution to ligand recognition [1].

Structural Features

No three-dimensional structure has been solved for this CBM family.

Functionalities

Ruminococcus flavefaciens CBM75_RfGH43, is a biding module of a protein containing a glycoside hydrolase family 43 (GH43) and a C-terminal dockerin module [1]. The GH43 catalytic domain, is a member of subfamily 16 (GH43_16) that is populated only with arabinofuranosidases [2]. Indeed, the catalytic module RfGH43 is active against 4-nitrophenyl-α-L-arabinofuranose but does not cleave arabinoxylans and arabinans, suggesting that this enzyme may target arabinofuranose residues that decorate other polysaccharides [1]. The CBMs specificity is consistent with the activity of the appended enzyme. Since CBM75_RfGH43 binds specifically to xyloglucan it was suggested that the enzyme GH43_16 may target arabinofuranose decorations present on xyloglucan from tomato [1].

Family Firsts

First Identified: CBM75_RfGH43 from Ruminococcus flavefaciens [1].
First Structural Characterization: No three-dimensional structure has been solved for this family.

References

All Medline abstracts: PubMed

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-* [[Author]]: ^^^Ana Luis^^^
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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.
+CBM75 is a small bacterial family containing only 3 members comprising around 290 amino acids and found exclusively in Ruminococci. The only family member characterized is CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' that specifically binds to xyloglucan <cite>Venditto2016</cite>. By isothermal titration calorimetry, the affinity to xyloglucan repeating unit XXXG (X comprises glucose decorated at O6 with xylose and G corresponds to undecorated glucose) is similar to the polysaccharide, suggesting that CBM75<sub>RfGH43</sub> has four binding sites that recognize the backbone glucose units. However, the specific binding to xyloglucan and not to other β-glucan polysaccharides indicates that at least some of the xylose side chains also have a major contribution to ligand recognition <cite>Venditto2016</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:''
+No three-dimensional structure has been solved for this CBM family.
-* '''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:''
+''Ruminococcus flavefaciens'' CBM75<sub>RfGH43</sub>, is a biding module of a protein containing a glycoside hydrolase family 43 ([[GH43]]) and a C-terminal dockerin module <cite>Venditto2016</cite>. The GH43 catalytic domain, is a member of subfamily 16 (GH43_16) that is populated only with arabinofuranosidases <cite>Mewis2016</cite>. Indeed, the catalytic module RfGH43 is active against 4-nitrophenyl-α-L-arabinofuranose but does not cleave arabinoxylans and arabinans, suggesting that this enzyme may target arabinofuranose residues that decorate other polysaccharides <cite>Venditto2016</cite>. The CBMs specificity is consistent with the activity of the appended enzyme. Since CBM75<sub>RfGH43</sub> binds specifically to xyloglucan it was suggested that the enzyme GH43_16 may target arabinofuranose decorations present on xyloglucan from tomato <cite>Venditto2016</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: CBM75<sub>RfGH43</sub> from ''Ruminococcus flavefaciens'' <cite>Venditto2016</cite>.
-:Insert archetype here, possibly including ''very brief'' synopsis.
+;First Structural Characterization: No three-dimensional structure has been solved for this family.
-;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Venditto2016 pmid=27298375
-#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. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
+#Mewis2016 pmid=26729713
-#Boraston2004 pmid=15214846
-#Hashimoto2006 pmid=17131061
-#Shoseyov2006 pmid=16760304
-#Guillen2010 pmid=19908036
-#Armenta2017 pmid=28547780
 </biblio>
 [[Category:Carbohydrate Binding Module Families|CBM075]]