Difference between revisions of "Carbohydrate Binding Module Family 75"

Revision as of 13:52, 8 May 2018

This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.

Author: ^^^Ana Luis^^^
Responsible Curator: ^^^Harry Gilbert^^^

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 do not cleave arabinoxylans and arabinans, suggesting that this enzyme may target arabinofuranose residues that decorate other polysaccharides [1]. The CBMs specificity is usually 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

@@ Line 17: / Line 17: @@
 == 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 do not cleave arabinoxylans and arabinans, suggesting that this enzyme may target arabinofuranose residues that decorate other polysaccharides <cite>Venditto2016</cite>. The CBMs specificity is usually 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]]