New to the CAZy classification? Read this first.
Want to learn more about CAZypedia? Read the CAZypedia 10th anniversary article in Glycobiology.

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Revision as of 21:01, 27 November 2013

Welcome to CAZypedia!
The Encyclopedia of Carbohydrate-Active Enzymes.
Cazypedia logo big.png

Purpose

CAZypedia has been initiated as a community-driven resource to assemble a comprehensive encyclopedia of the "CAZymes," the carbohydrate-active enzymes and associated carbohydrate-binding modules involved in the synthesis and degradation of complex carbohydrates. CAZypedia is inspired by, and closely connected with, the actively curated CAZy Database. It's probably fair to say that CAZypedians are, like our friends at the CAZy DB, a group of "biocurators."
If you are new to the CAZyme classification, "Sorting the Diverse" by Professors Gideon Davies and Michael Sinnott (The Biochemist, 2008, vol. 30, part 4, pp. 26-32) provides an excellent introduction and historical perspective.

Content

CAZypedia initially focussed on the Glycoside Hydrolase Families defined in the CAZy Database, and we continue to strive for complete coverage of this diverse class of enzymes. Other catabolic and anabolic CAZymes, as well as Auxiliary redox enzymes and non-catalytic Carbohydrate Binding Modules, continue to be incorporated as interest and engagement from the scientific community grows. In addition, there is a Lexicon of terms relevant to CAZymes and carbohydrate chemistry.
These and other aspects of CAZypedia's content can be accessed through the menus on the left side of each page.

How CAZypedia works

CAZypedia is built on authoring and editing principles similar to those of other expert-based online encyclopedias (cf. Citizendium, Scholarpedia). All contributors to CAZypedia, from the Authors to the Board of Curators, are experts in the field. Transparency is achieved through the use of contributors' real names and published biographies in CAZypedia. Individual entries in CAZypedia are managed by Responsible Curators, who are responsible for selecting expert Authors and coordinating author contributions on individual pages. Selection of Responsible Curators, based on their specialist expertise and ability to participate in the active maintenance of entry content, is handled by the Senior Curators.
More information on CAZypedia's content and editorial policies is available here.
A short lecture and a set of slides presenting CAZypedia are freely available here.
An article describing CAZypedia's genesis and evolution has been published in the journal Glycobiology.

Contact

If you would like to get involved with CAZypedia or suggest an improvement, please contact the Board of Curators.

Latest news

22 September 2020: Like PLs, but different: We are happy to announce the completion of a new Lexicon page on Polysaccharide epimerases today. Margrethe Gaardlos spearheaded the composition of this new page, with input from co-author Anne Tøndervik and Responsible Curator Finn Lillelund Aachmann. Although they are not categorized into families in the CAZy system, Polysaccharide epimerases bear a lot of structural and mechanistic similarity to Polysaccharide Lyases: Instead of catalyzing an elimination reaction to break poly-uronic acid chains, Polysaccharide epimerases simply use the first part of the PL mechanism to remove and re-add the C-5 proton. The resulting change in the configuration of the C-6 carboxylate has major impacts on polysaccharide structure and properties. The Norwegian team has done a tremendous job in capturing the broad history of these enzymes, including their diverse substrate specificities and structures (and over 130 references!), which you can read all about here. (We also thank Mirjam Czjzek for championing the inclusion of the "PEs" in CAZYpedia.)

6 August 2020: A beta-1,3-glucanase family with a deep history: Julie Grondin's Glycoside Hydrolase Family 81 page was Curator Approved by Al Boraston today. GH81 has a long history of discovery and mechanistic study, including by original CAZypedian and Cellulase/CAZyme GRC co-founder David Wilson and co-workers. By capturing a phenomenal number of oligosaccharide complexes, Al's group has recently provided detailed molecular description of how enzymes in this family specifically recognize the helical structure adopted by beta-1,3-glucans. Be sure to check out the GH81 page to get the full history of the contributions of a number of groups world-wide to our knowledge of this family.


23 July 2020: Another CE family page from our friends at WLU! The Carbohydrate Esterase Family 7 page was finalized and promoted to Curator Approved status today. Joel Weadge and Michael Suits have been leading the completion of a bunch of CE pages with the help of keen students from Wilfred Laurier University (see CE3, CE4, and CE9). This time, Emily Rodriguez produced the CE7 page, which encompasses acetyl xylan esterases and cephalosporin-C deacetylases. Learn more about the specificity, mechanism, and three-dimensional structure of CE7 enzymes here.


19 June 2020: Three additional alginate lyase families! The number of PL family pages in CAZypedia continues to grow with the promotion of the Polysaccharide Lyase Family 6, Polysaccharide Lyase Family 15, and Polysaccharide Lyase Family 17 pages to Curator Approved status today. We thank Emil G.P. Stender for his hard work in tackling this trifecta of bacterial alginate lyase families (including some heparin/heparan sulfate lyases from the human gut microbiota in PL15), which were vetted Responsible Curator Birte Svensson. Dig into the details of these families on the PL6, PL15, and PL17 pages, in comparison with the recently completed PL7 page (see previous news item, below).


17 June 2020: PLs from the sea. The Polysaccharide Lyase Family 7 page, which was written by Nadine Gerlach, was promoted to completed by Curator Approved status today by Jan-Hendrik Hehemann. The founding member of PL7, an alginate lyase, was characterized way back in 1993 by a team notably including CAZypedian Gurvan Michel. Alginate is heteropolysaccharide from brown algae and mucoid bacteria, consisting of beta-d-mannuronate (M) and alpha-l-guluronate (G) residues in varying ratios and intra-chain distributions, depending on the source. As a result, PL7 members exhibit mannuronate, guluronate, or mixed link specificity. Read more about the deep history of enzymolgoy and structural biology of PL7 here, including seminal work by Jan-Hendrik showing the horizontal gene transfer of these enzymes into the human gut microbiota and other marine bacteria.


16 June 2020: From rotting plants to vegetable digestion in the gut. The Polysaccharide Lyase Family 9 page was completed by Ana Luis and upgraded to Curator Approved status today by Wade Abbott. PL9 was originally identified and characterized as part of the pectin-degrading machinery from the plant pathogenic bacterium Dickeya dadantii (Erwinia chrysanthemi), including seminal structural work by Richard Pickersgill and colleagues. More recently Ana and Wade, as part of a big team involving other CAZypedians Jonathon Briggs, Didier Ndeh, Alan Cartmell, Bernard Henrissat, and Harry Gilbert, shed new light on the role of PL9 members in the human gut microbiota. Take some time to learn more about the long and rich history of Polysaccharide Lyase Family 9!


> older news

Dedication

CAZypedia is dedicated to the late Prof. Bruce Stone, whose enthusiasm to create a comprehensive encyclopedia of carbohydrate-active enzymes was essential in the genesis of this project.