The February 2024 update of CAZy
This month, we are welcoming a novel GH family, GH189 after the functional and structural characterization by Tanaka et al. (PMID=38300345) of a transglycosidase activity for a module belonging to this family, distantly related to GH144 and GH162. This team also recently deposited a manuscript to bioRxiv about this superfamily. GH189 distinguished by being systematically part of a trimodular proteins involved in the cyclic β-1,2-glucan syntesis pathway, for which another nice manuscript could be found in bioRxiv.
We also released a new GT family, GT118, discovered by Walklett et al. (PMID=38224120), as well as 17 bacterial polysaccharide polymerase families, GT119 to GT135, long-overdue but which required in-depth sequence analyses, to be published in Communications Biology by Meitil and coworkers.
Also, for those who missed it : end of 2023, we released on CAZy.org our expert annotation of the eukaryotic genomes sequenced by JGI after publication, including both MycoCosm and PhycoCosm projects ! This huge annotation effort is accomplished by Bernard and Elodie. We hope you’ll appreciate it.
The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
Online since 1998, CAZy is a specialist database dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes).
CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank.
New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description.
An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. Please let us know if some families have escaped our attention, we will be happy to add them !
For a more extensive encyclopedic resource on the particular features of carbohydrate active enzymes, please visit CAZypedia, a web site driven by the scientific community that studies these enzymes.
PULDB is a database of Polysaccharide Utilization Loci (PULs) in Bacteroidetes. PULDB displays information on experimentally determined and predicted PULs for a number of Bacteroidetes genomes.
A new reference for the CAZy database : We summarized the recent changes in the CAZy database, and evolution during the last eight years in an article published the Nucleic Acids Research (Database Issue), with a specific focus on functional annotations.
Read the full paper.
Enzyme Classes currently covered
Modules that catalyze the breakdown, biosynthesis or modification of carbohydrates and glycoconjugates :
Glycoside Hydrolases (GHs) : hydrolysis and/or rearrangement of glycosidic bonds (see CAZypedia definition)
GlycosylTransferases (GTs) : formation of glycosidic bonds (see definition)
Polysaccharide Lyases (PLs) : non-hydrolytic cleavage of glycosidic bonds
Carbohydrate Esterases (CEs) : hydrolysis of carbohydrate esters
Auxiliary Activities (AAs) : redox enzymes that act in conjunction with CAZymes.
Associated Modules currently covered
Carbohydrate-active enzymes often display a modular structure with non-catalytic modules appended to the enzymes above
Carbohydrate-Binding Modules (CBMs) : adhesion to carbohydrates
Genome analysis by CAZy
Family distribution and/or protein listings of the carbohydrate-active enzymes and associated proteins identified in genomes
Genomes by Kingdom :
Last Functions released
alginate lyase (AlyC6’) | WP_016791256.1 | 4.2.2.3 | pubmed |
alginate lyase (AlyC6’) | WP_016791256.1 | 4.2.2.11 | pubmed |
b-glycosidase (TY87_18135) | PJE53865.1 | 3.2.1.21 3.2.1.23 | pubmed pubmed |
endoxylanase (denovogenes_5086; IKI06_02965) | MBR7030185.1 | 3.2.1.8 | pubmed |
CelXyn2 / IKP37_07625 | MBR6042486.1 | 3.2.1.73 | pubmed |
b-galactosidase | WP_076345996.1 | 3.2.1.23 | pubmed |
b-galactosidase (Gal; GYB58_00550) | MBR9790212.1 | 3.2.1.23 | pubmed |
exo-b-1,3/4/6-galactanase / a-L-arabinopyranosidase (PpBGal42A) | WP_040101590.1 | 3.2.1.23 3.2.1.88 | pubmed pubmed |
bifunctional acetylxylan esterase and feruloyl esterase (DmCE1B; HMPREF9456_02279) | EGK06015.1 | 3.1.1.72 3.1.1.73 | pubmed pubmed |
acetylxylan esterase (DmCE6A; HMPREF9456_02270) | EGK06006.1 | 3.1.1.72 | pubmed |
feruloyl esterase (DmCE1A; HMPREF9456_02268) | EGK06004.1 | 3.1.1.73 | pubmed |
mixed-linkage xylan-specific endo-b-1,4-xylanase (PpXyn26A; DX130_15985) | REK75131.1 WP_116047020.1 | 3.2.1.- | pubmed |
mixed-linkage xylan-specific endo-b-1,4-xylanase (CaXyn26A) | WP_077338539.1 | 3.2.1.- | pubmed |
mixed-linkage xylan-specific endo-b-1,4-xylanase (CeXyn26A; M4I21_06905) | MCL5245529.1 WP_249558383.1 | 3.2.1.- | pubmed |
3-O-b-L-arabinopyranosyl-a-L-arabinofuranosidase (AAfase; MCC10289_0425) | WP_065438160.1 BDV32471.1 | 3.2.1.- | pubmed |