Difference between revisions of "Carbohydrate Binding Module Family 89"

Revision as of 06:34, 21 June 2023

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CAZy DB link
https://www.cazy.org/CBM89.html

Ligand specificities

CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) Cabral202Cabral202. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates Cabral202Cabral202.

Structural Features

Content in this section should include, in paragraph form, a description of:

Fold: The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) Cabral202Cabral202 displays a parallel β-helix fold, consisting of 14 complete helical turns.

Features of ligand binding: A Ca²⁺ was found in the structure, connecting the 11^th and 12^th turns (https://www.rcsb.org/structure/7JVI). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca2+ binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan Cabral202Cabral202. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding Cabral202Cabral202.

Functionalities

Content in this section should include, in paragraph form, a description of:

Functional role of CBM: In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan Cabral202Cabral202. The cluster encodes the CapCBM89-GH10 and two exo-enzymes from GH43 and GH97 families <ref>Cabral2022<ref>. The GH10 domain is active on arabinoxylan and xylan, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case Cabral202Cabral202.
Most Common Associated Modules: 1. Glycoside Hydrolases from family GH10.

Family Firsts

First Identified The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome Cabral202Cabral202.
First Structural Characterization The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome Cabral202Cabral202.

References

pmid= 35110564
[Cabral20222]

@@ 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.
+CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) <cite>Cabral202Cabral202<cite>. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates <cite>Cabral202Cabral202<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:''
-* '''Fold:''' Structural fold (beta trefoil, beta sandwich, etc.)
+* '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <cite>Cabral202Cabral202<cite> displays a parallel β-helix fold, consisting of 14 complete helical turns.
-* '''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.
+* '''Features of ligand binding:''' A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> turns (https://www.rcsb.org/structure/7JVI). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca2+ binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral202Cabral202<cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding <cite>Cabral202Cabral202<cite>.
 == Functionalities ==
 ''Content in this section should include, in paragraph form, a description of:''
-* '''Functional role of CBM:''' Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
+* '''Functional role of CBM:''' In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan <cite>Cabral202Cabral202<cite>. The cluster encodes the CapCBM89-GH10 and two exo-enzymes from GH43 and GH97 families <ref>Cabral2022<ref>. The GH10 domain is active on arabinoxylan and xylan, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case <cite>Cabral202Cabral202<cite>.
-* '''Most Common Associated Modules:''' 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
+* '''Most Common Associated Modules:''' 1. Glycoside Hydrolases from family GH10.
-* '''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 The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome <cite>Cabral202Cabral202<cite>.
-:Insert archetype here, possibly including ''very brief'' synopsis.
+;First Structural Characterization The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome <cite>Cabral202Cabral202<cite>.
-;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Cabral20222 pmid= 35110564
-#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 Download PDF version].
-#Boraston2004 pmid=15214846
-#Hashimoto2006 pmid=17131061
-#Shoseyov2006 pmid=16760304
-#Guillen2010 pmid=19908036
-#Armenta2017 pmid=28547780
 </biblio>
 <!-- Do not delete this Category tag -->
 [[Category:Carbohydrate Binding Module Families|CBM089]]