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Difference between revisions of "Carbohydrate Binding Module Family 89"
| Line 21: | Line 21: | ||
== Structural Features == | == Structural Features == | ||
''Content in this section should include, in paragraph form, a description of:'' | ''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) <cite> | + | * '''Fold:''' The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) <cite>Cabral2022<cite> displays a parallel β-helix fold, consisting of 14 complete helical turns. |
| − | * '''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> | + | * '''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>Cabral202Cabral2022<cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding <cite>Cabral2022<cite>. |
== Functionalities == | == Functionalities == | ||
| Line 32: | Line 32: | ||
== Family Firsts == | == Family Firsts == | ||
| − | ;First Identified The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome <cite>Cabral202Cabral202<cite>. | + | ''';First Identified''' |
| − | ;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>. | + | The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome <cite>Cabral202Cabral202<cite>. |
| + | ''';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>. | ||
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Cabral2022 pmid= 35110564 |
</biblio> | </biblio> | ||
Revision as of 06:38, 21 June 2023
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.
- Authors: Mariana Abrahão Bueno de Morais and Gabriela Felix Persinoti
- Responsible Curator: Mario Murakami
| 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) Cabral2022 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 11th and 12th 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 Cabral202Cabral2022. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding Cabral2022.
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
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pmid= 35110564