|
|
| (138 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| − | '''10 June 2020:''' ''Back to the origins of CAZy.'' A page on a [[Carbohydrate-binding modules|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 [[Carbohydrate-binding_modules#Types|type A]] [[CBM5]] members interacting with chitin. Thank you to '''[[User:Manjeet Kaur|Manjeet Kaur]]''' for [[author]]ing the page and to '''[[User:Appa Rao Podile|Appa Rao Podile]]''' for acting as [[Responsible Curator]]. ''Read up on this old school family of CBMs '''[[CBM5|here]]'''.'' | + | '''19 July 2024:''' ''Chalk-up one more for the GTs!'' The '''[[Glycosyltransferase Family 47]]''' page joined the small group of [[Curator Approved]] [[Glycosyltransferase Families]] pages in ''CAZypedia'' today. This entry was [[author]]ed by Ph.D. students '''[[User:Daniel Tehrani|Daniel Tehrani]]''' and '''[[User:Charlie Corulli|Charlie Corulli]]''', and [[Responsible Curator|Curated]] by '''[[User:Breeanna Urbanowicz|Breeanna Urbanowicz]]''' with input from '''[https://ccrc.uga.edu/team/kelley-moremen/ Kelley Moremen]'''. Widely represented in plants, '''[[GT47]]''' members are anomer-[[inverting]] [[glycosyltransferases]], which are involved in the biosynthesis of several cell wall matrix polysaccharides. Representatives from mammals are involved in heparin biosynthesis. Correspondingly, members of [[GH47]] have diverse substrate specificities, including the transfer of both anionic and neutral monosaccharides to polysaccharides. ''This is a great example where two keen Ph.D. students worked with their supervisors to create a valuable page for the scientific community. We encourage others to follow their lead, on your favorite family!'' |
| | ---- | | ---- |
| − | '''10 June 2020:''' ''Continued growth among the esterases.'' The '''[[Carbohydrate Esterase Family 3]]''' page, [[Author]]ed by grad student '''[[User:Stefen Stangherlin|Stefen Stangherlin]]''', was finalized and [[Curator Approved]] by '''[[User:Joel Weadge|Joel Weadge]]''' and '''[[User:Michael Suits|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 '''[[User:Stefen Stangherlin|Stefen]]''', '''[[User:Joel Weadge|Joel]]''', and '''[[User:Michael Suits|Mike]]''' for contributing yet another page to the growing [[Carbohydrate Esterase Families|CE family section]] in CAZypedia - read more on CE3 '''[[Carbohydrate Esterase Family 3|here]]'''.'' | + | '''9 July 2024:''' ''Yet another new family of beta-1,2-glucan-active enzymes!'' Today, '''[[User:Masahiro Nakajima|Masahiro Nakajima]]''' [[Curator Approved]] the '''[[Glycoside Hydrolase Family 186]]''' page by '''[[User:Sei Motouchi|Sei Motouchi]]'''. '''[[GH186]]''' is a family of anomer-[[inverting]] enzymes from bacteria, members of which are specific for beta-1,2-glucans. Intriguingly, although some [[GH186]] members work as classic [[glycoside hydrolases]], others perform transglycosylation by wrapping the sugar chain around in the active-site, to position the 6-OH group of a terminal glucosyl unit for direct attack. Also notable, [[GH186]] members appear to use an extended chain of water molecules to relay acceptor deprotonation by the [[general base]] residue, ''i.e.'' a [https://en.wikipedia.org/wiki/Grotthuss_mechanism Grotthuss mechanism]. ''Check out the '''[[GH186]]''' page to learn more about these interesting enzymes, and make sure to see the [[GH189]], [[GH144]], and [[GH162]] pages from this same group.'' |
| | | | |
| | ---- | | ---- |
| − | '''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 [[Auxiliary Activity Families|lytic polysaccharide monooxygenases]] but also in non-CAZy enzymes. The page was authored by '''[[User:Marie Sofie Moeller|Marie Sofie Møller]]''' with '''[[User:Birte Svensson|Birte Svensson]]''' and '''[[User:Stefan Janecek|Stefan Janecek]]''' acting as responsible curators. ''Find out more on this starch-interacting family '''[[CBM20|here]]'''.'' | + | '''2 May 2024:''' ''CBDs I to X... A major milestone!'' '''CBM families 1 to 10 are now complete!''' These are the old CBD (cellulose-binding domain) families, which used to have roman numerals as part of their nomenclature. A special thank you to all the authors and responsible curators who have contributed to this major milestone. Go have a peek at each of these old school families on their respective ''CAZypedia'' pages: '''[[CBM1]], [[CBM2]], [[CBM3]], [[CBM4]], [[CBM5]], [[CBM6]], [[CBM7]], [[CBM8]], [[CBM9]], and [[CBM10]]'''. |
| − | | |
| − | ----
| |
| − | '''15 May 2020:''' ''More on beta(1,3)-glucanases.'' The '''[[Glycoside Hydrolase Family 64]]''' page, [[Author]]ed by '''[[User:Julie Grondin|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 '''[[User:Bernard Henrissat|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|Glycoside Hydrolase Family 64 here]]'''.'' | |
| − | ----
| |
| − | '''11 May 2020:''' ''Three more from the gut.'' '''[[User:Alan Cartmell|Alan Cartmell]]''' completed no less than three new [[Glycoside Hydrolase Families|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 '''[[User:Harry Gilbert|Harry Gilbert]]'s''' group, to which '''[[User:Alan Cartmell|Alan]]''' contributed defining crystallography. '''[[User:Alan Cartmell|Alan]]''' has also taken over the duty of [[Responsible Curator]] of these pages following the retirement of the venerable '''[[User:Harry Gilbert|Professor Gilbert]]''', one of ''CAZypedia's'' [[CAZypedia:History|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 Families|Carbohydrate Esterase Family]] page in the series, '''[[CE1]]''', was [[Curator Approved]] today. [[Author]]ed by '''[[User:Casper Wilkens|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]] '''[[User:Kazune Tamura|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 '''[[User:Kazune Tamura|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 '''[[Glycoside Hydrolase Family 158|here]]'''.''
| |
| − | ----
| |
| − | '''8 April 2020:''' ''Another new one from the gut.'' The '''[[Glycoside Hydrolase Family 164]]''' page, which was [[author]]ed by '''[[User:Zachary Armstrong|Zachary Armstrong]]''', was upgraded to [[Curator Approved]] status by [[Responsible Curator]] '''[[User:Gideon Davies|Gideon Davies]]''' today. '''[[Glycoside Hydrolase Family 164]]''' is yet another newly discovered [[Glycoside Hydrolase Families|GH family]] from a human gut bacterium - this time through a large-scale effort by teams at AFMB and CERMAV spearheaded by [[User:Bernard Henrissat|Bernard Henrissat]]. The founding member of '''[[GH164]]''' is a beta-mannosidase from ''Bacteroides salyersiae'', on which '''[[User:Zachary Armstrong|Zach]]''' and '''[[User:Gideon Davies|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 '''[[Glycoside Hydrolase Family 164|here]]'''.''
| |
| | ---- | | ---- |
19 July 2024: Chalk-up one more for the GTs! The Glycosyltransferase Family 47 page joined the small group of Curator Approved Glycosyltransferase Families pages in CAZypedia today. This entry was authored by Ph.D. students Daniel Tehrani and Charlie Corulli, and Curated by Breeanna Urbanowicz with input from Kelley Moremen. Widely represented in plants, GT47 members are anomer-inverting glycosyltransferases, which are involved in the biosynthesis of several cell wall matrix polysaccharides. Representatives from mammals are involved in heparin biosynthesis. Correspondingly, members of GH47 have diverse substrate specificities, including the transfer of both anionic and neutral monosaccharides to polysaccharides. This is a great example where two keen Ph.D. students worked with their supervisors to create a valuable page for the scientific community. We encourage others to follow their lead, on your favorite family!
9 July 2024: Yet another new family of beta-1,2-glucan-active enzymes! Today, Masahiro Nakajima Curator Approved the Glycoside Hydrolase Family 186 page by Sei Motouchi. GH186 is a family of anomer-inverting enzymes from bacteria, members of which are specific for beta-1,2-glucans. Intriguingly, although some GH186 members work as classic glycoside hydrolases, others perform transglycosylation by wrapping the sugar chain around in the active-site, to position the 6-OH group of a terminal glucosyl unit for direct attack. Also notable, GH186 members appear to use an extended chain of water molecules to relay acceptor deprotonation by the general base residue, i.e. a Grotthuss mechanism. Check out the GH186 page to learn more about these interesting enzymes, and make sure to see the GH189, GH144, and GH162 pages from this same group.
2 May 2024: CBDs I to X... A major milestone! CBM families 1 to 10 are now complete! These are the old CBD (cellulose-binding domain) families, which used to have roman numerals as part of their nomenclature. A special thank you to all the authors and responsible curators who have contributed to this major milestone. Go have a peek at each of these old school families on their respective CAZypedia pages: CBM1, CBM2, CBM3, CBM4, CBM5, CBM6, CBM7, CBM8, CBM9, and CBM10.