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 horixontal 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!
13 June 2020: A GH family with lots of unknowns. Glycoside Hydrolase Family 151 is a fairly old family of alpha-l-fucosidases in the CAZy classification, yet a number of key mechanistic and structure-function questions remain to be explored, as we learn in the GH151 page completed today by Casper Wilkens, David Teze, and Birgitte Zeuner. See a current example of how information on Glycoside Hydrolase Families is constantly evolving here.
10 June 2020: A new Senior Curator. Today we welcome Elizabeth Ficko-Blean as a Senior Curator in CAZypedia. Over the past ca. 3 years, Liz has been the major force driving the production of the many new Carbohydrate Binding Module Family pages now in CAZypedia through the active recruitment of Authors and Responsible Curators, as well as a lot of subsequent editorial work.
10 June 2020: Back to the origins of CAZy. A page on a Carbohydrate Binding Module family that was first classified as Cellulose-Binding Domain Family V (CBD V), and has since been renamed in CAZy as Carbohydrate Binding Module Family 5, is now on-line in CAZypedia. While originally considered to be cellulose-binding domains, there are now several examples of the type A CBM5 members interacting with chitin. Thank you to Manjeet Kaur for authoring the page and to Appa Rao Podile for acting as Responsible Curator. Read up on this old school family of CBMs here.
10 June 2020: Continued growth among the esterases. The Carbohydrate Esterase Family 3 page, Authored by grad student Stefen Stangherlin, was finalized and Curator Approved by Joel Weadge and Michael Suits today. CE3 comprises a group of specific acetyl-xylan esterases with a rich history of initial discovery, mechanistic analysis, and structural characterization. We thank Stefen, Joel, and Mike for contributing yet another page to the growing CE family section in CAZypedia - read more on CE3 here.
15 May 2020: CBM20 for 2020! The multifunctional starch-disrupting, starch-binding and enzyme targeting CBM20 family is now up and running in CAZypedia. These pervasive CBMs have been identified in CAZy families including glycoside hydrolases and lytic polysaccharide monooxygenases but also in non-CAZy enzymes. The page was authored by Marie Sofie Møller with Birte Svensson and Stefan Janecek acting as responsible curators. Find out more on this starch-interacting family here.
15 May 2020: More on beta(1,3)-glucanases. The Glycoside Hydrolase Family 64 page, Authored by Julie Grondin, was completed and Curator Approved today. GH64 comprises a group of β-1,3-glucanases, primarily from bacteria.The archetype of this family was originally cloned from a Streptomyces species in the late 1990's and was the subject of mechanistic and structural analysis through the first decade of the new millenium. Notably, analysis by a team led by Bernard Henrissat defined that this enzyme, and thus family, uses an inverting mechanism, further disntiguishing it from well-known retaining beta(1,3)-glucanases of GH16, GH17, and others, including the recently described GH158 beta(1,3)-glucanases reported below. Read more about the unique Glycoside Hydrolase Family 64 here.
11 May 2020: Three more from the gut. Alan Cartmell completed no less than three new Glycoside Hydrolase Family pages on this day. Glycoside Hydrolase Family 137, Glycoside Hydrolase Family 140, and Glycoside Hydrolase Family 145 were all created from a series of studies of Polysacchardie Utilization Loci from human gut bacteria by Harry Gilbert's group, to which Alan contributed defining crystallography. Alan has also taken over the duty of Responsible Curator of these pages following the retirement of the venerable Professor Gilbert, one of CAZypedia's founding Senior Curators. Read more about the substrate specificity and structural biology of these three diverse families on their corresponding pages.
6 May 2020: CE #1! The first Carbohydrate Esterase Family page in the series, CE1, was Curator Approved today. Authored by Casper Wilkens, the Carbohydrate Esterase Family 1 page describes an old family of carbohydrate-specific and other esterases, members of which were identified through classical biochemistry before the present age of easy gene cloning and sequencing. Carbohydrate-active members of CE1 include acetyl xylan esterases, cinnamoyl esterases, and feruloyl esterases responsible for hydrolyzing pendant acyl groups from plant cell wall matrix glycans (hemicelluloses). Read more about the long history of Carbohydrate Esterase Family 1 here.
10 April 2020: Yet another new one from the gut. Today, Author Kazune Tamura completed the Glycoside Hydrolase Family 158 page. GH158 emerged in 2019 from a high-throughput biochemical survey of sequences identified as distantly related to glycoside hydrolases by the CAZy team, who first demonstrated endo-beta(1,3)-glucanase activity for the founding member of the family from the human gut bacterium Victivallis vadensis. Contemporaneously, analysis of homolgos from human gut Bacteroides species by Guillaume Dejean and Kazune Tamura resolved details of the specificity, mechanism, and tertiary structure of GH158 members in Polysaccharide Utilization Loci. Read about the detailed history and juicy details of this new GH family here.
8 April 2020: Another new one from the gut. The Glycoside Hydrolase Family 164 page, which was authored by Zachary Armstrong, was upgraded to Curator Approved status by Responsible Curator Gideon Davies today. Glycoside Hydrolase Family 164 is yet another newly discovered GH family from a human gut bacterium - this time through a large-scale effort by teams at AFMB and CERMAV spearheaded by Bernard Henrissat. The founding member of GH164 is a beta-mannosidase from Bacteroides salyersiae, on which Zach and Gideon performed a classic mechanistic and structural analysis to define the central aspects of catalysis in this new family. Read more about this new - and currently tiny - GH family here.
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