The Carbohydrate-active Enzymes Database (CAZy) in 2013

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2013 Nov 26

PMID 24270786

Citations 2702

Authors

Vincent Lombard

Hemalatha Golaconda Ramulu

Elodie Drula

Pedro M Coutinho

Bernard Henrissat

Affiliations

Soon will be listed here.

Abstract

The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3D structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides. Functional and 3D structural information is added and curated on a regular basis based on the available literature. In addition to the use of the database by enzymologists seeking curated information on CAZymes, the dissemination of a stable nomenclature for these enzymes is probably a major contribution of CAZy. The past few years have seen the expansion of the CAZy classification scheme to new families, the development of subfamilies in several families and the power of CAZy for the analysis of genomes and metagenomes. This article outlines the changes that have occurred in CAZy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes.

Citing Articles

Genome mining the black-yeast Aureobasidium pullulans NRRL 62031 for biotechnological traits.

Xiao D, Driller M, Stein K, Blank L, Tiso T BMC Genomics. 2025; 26(1):244.

PMID: 40082747 PMC: 11905612. DOI: 10.1186/s12864-025-11395-2.

Genome Sequence, Comparative Genome Analysis, and Expression Profiling of the Chitinase GH18 Gene Family in Bd01.

Zhu T, Hussain M, Ning J, Chen X, Shi C, Yang D Int J Mol Sci. 2025; 26(5).

PMID: 40076665 PMC: 11900538. DOI: 10.3390/ijms26052031.

Gut Microbiota of Ruminants and Monogastric Livestock: An Overview.

Tardiolo G, La Fauci D, Riggio V, Daghio M, Di Salvo E, Zumbo A Animals (Basel). 2025; 15(5).

PMID: 40076043 PMC: 11899476. DOI: 10.3390/ani15050758.

Genome-wide identification of invertase genes in sweetpotato and its response to nitrogen and planting densities.

Hu Z, He P, Li Y, Liu H, Ahmad R, Ali I BMC Plant Biol. 2025; 25(1):281.

PMID: 40033202 PMC: 11877694. DOI: 10.1186/s12870-025-06295-2.

Gut Microecology of Four Sympatric Desert Rodents Varies by Diet.

Chu D, Zhang H, Shang Z, Liu N, Fu H, Yuan S Ecol Evol. 2025; 15(3):e70992.

PMID: 40027415 PMC: 11868701. DOI: 10.1002/ece3.70992.

References

Petrescu A, Petrescu S, Dwek R, Wormald M . A statistical analysis of N- and O-glycan linkage conformations from crystallographic data. Glycobiology. 1999; 9(4):343-52. DOI: 10.1093/glycob/9.4.343. View

Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho P, Henrissat B . A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J. 2010; 432(3):437-44. DOI: 10.1042/BJ20101185. View

Campbell J, Davies G, Bulone V, Henrissat B . A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem J. 1997; 326 ( Pt 3):929-39. PMC: 1218753. DOI: 10.1042/bj3260929u. View

Coutinho P, Deleury E, Davies G, Henrissat B . An evolving hierarchical family classification for glycosyltransferases. J Mol Biol. 2003; 328(2):307-17. DOI: 10.1016/s0022-2836(03)00307-3. View

Cantarel B, Lombard V, Henrissat B . Complex carbohydrate utilization by the healthy human microbiome. PLoS One. 2012; 7(6):e28742. PMC: 3374616. DOI: 10.1371/journal.pone.0028742. View

Cantarel B, Coutinho P, Rancurel C, Bernard T, Lombard V, Henrissat B . The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2008; 37(Database issue):D233-8. PMC: 2686590. DOI: 10.1093/nar/gkn663. View

Lozupone C, Hamady M, Cantarel B, Coutinho P, Henrissat B, Gordon J . The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A. 2008; 105(39):15076-81. PMC: 2546442. DOI: 10.1073/pnas.0807339105. View

Henrissat B . A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J. 1991; 280 ( Pt 2):309-16. PMC: 1130547. DOI: 10.1042/bj2800309. View

St John F, Gonzalez J, Pozharski E . Consolidation of glycosyl hydrolase family 30: a dual domain 4/7 hydrolase family consisting of two structurally distinct groups. FEBS Lett. 2010; 584(21):4435-41. DOI: 10.1016/j.febslet.2010.09.051. View

10.

Levasseur A, Drula E, Lombard V, Coutinho P, Henrissat B . Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels. 2013; 6(1):41. PMC: 3620520. DOI: 10.1186/1754-6834-6-41. View

11.

Hart G, Copeland R . Glycomics hits the big time. Cell. 2010; 143(5):672-6. PMC: 3008369. DOI: 10.1016/j.cell.2010.11.008. View

12.

Hunter S, Jones P, Mitchell A, Apweiler R, Attwood T, Bateman A . InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2011; 40(Database issue):D306-12. PMC: 3245097. DOI: 10.1093/nar/gkr948. View

13.

Ohm R, Feau N, Henrissat B, Schoch C, Horwitz B, Barry K . Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog. 2012; 8(12):e1003037. PMC: 3516569. DOI: 10.1371/journal.ppat.1003037. View

14.

Aspeborg H, Coutinho P, Wang Y, Brumer 3rd H, Henrissat B . Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol. 2012; 12:186. PMC: 3526467. DOI: 10.1186/1471-2148-12-186. View

15.

Lutteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth C . GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology. 2005; 16(5):71R-81R. DOI: 10.1093/glycob/cwj049. View

16.

Henrissat B, Bairoch A . New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J. 1993; 293 ( Pt 3):781-8. PMC: 1134435. DOI: 10.1042/bj2930781. View

17.

Henrissat B, Davies G . Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol. 1997; 7(5):637-44. DOI: 10.1016/s0959-440x(97)80072-3. View

18.

Stam M, Danchin E, Rancurel C, Coutinho P, Henrissat B . Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Eng Des Sel. 2006; 19(12):555-62. DOI: 10.1093/protein/gzl044. View

19.

Lutteke T, von der Lieth C . pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files. BMC Bioinformatics. 2004; 5:69. PMC: 441419. DOI: 10.1186/1471-2105-5-69. View

20.

Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y . dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012; 40(Web Server issue):W445-51. PMC: 3394287. DOI: 10.1093/nar/gks479. View