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Difference between revisions of "Template:News"

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'''2 December 2016:''' ''A new CAZyme-specific journal:'' The journal ''[https://www.degruyter.com/view/j/amylase Amylase]'' has been recently launched under the editorial leadership of [[User:Stefan Janecek|Stefan Janecek]] and a number of other CAZypedians, including [[User:Bernard Henrissat|Bernard Henrissat]], [[User:Magali Remaud-Simeon|Magali Remaud-Simeon]], [[User:Birte Svensson|Birte Svensson]], [[User:Pedro Coutinho|Pedro Coutinho]], and [[User:Leila LoLeggio|Leila LoLeggio]].  ''[https://www.degruyter.com/view/j/amylase Amylase]'' is an open access journal that will focus on the biochemistry and biotechnology of starch hydrolases and related alpha-glucan-active enzymes, such as those from '''[[GH13]]''', '''[[GH70]]''', and '''[[GH77]]''' ([[Clan]] GH-H), as well as '''[[GH57]]''', '''[[GH119]]''', '''[[GH14]]''', '''[[GH15]]''', and '''[[GH31]]'''.  Visit the ''[https://www.degruyter.com/view/j/amylase Amylase]'' homepage for more information on the scope of the journal and details on how to [http://www.editorialmanager.com/amylase/ submit manuscripts for publication].
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'''1 November 2024:''' ''Is this a world record? Six CAZypedia families in one fell swoop!'' The '''[[CBM47]], [[CBM70]], [[CBM96]], [[CBM105]], [[CBM106]] and [[PL44]]''' ''CAZypedia'' pages are now flipped to [[Curator Approved]] status. What do these diverse families from diverse origins with diverse binding specificities have in common? Astonishingly, at least one characterized member from each family interacts with a charged glycan! '''[[User:Wenwen Tao|Wenwen Tao]]''' authored the [[CBM47]], [[CBM96]] and [[CBM106]] pages, '''[[User:Menghui Sun|Menghui Sun]]''' authored the [[CBM70]] page, '''[[User:Guanchen Liu|Guanchen Liu]]''' authored the [[CBM105]] page and '''[[User:Jinhang Zhou|Jinhang Zhou]]''' authored the [[PL44]] page.  All this under the responsible curatorship of '''[[User:Yaoguang Chang|Yaoguang Chang]]'''. ''Dive into these diverse families on their respective ''CAZypedia'' pages: '''[[CBM47]], [[CBM70]], [[CBM96]], [[CBM105]], [[CBM106]] and [[PL44]]!'''''
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'''25 October 2024:''' ''Laminariawesome!'' Check out two new marine families of CBMs, '''[[CBM102]]''' and '''[[CBM103]]''', now on ''CAZypedia'' which have an ecological role in bacterial degradation of laminarin during phytoplankton blooms.  Some function as surface glycan binding proteins but others have roles in targeting their appended catalytic modules to substrate.  Both pages were [[author]]ed by '''[[User:Marie-Katherin Zuehlke|Marie-Katherin Zühlke]]'''. ''Read up on these environmentally important CBMs on their respective [[CBM102]] and [[CBM103]] pages!''
 
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'''29 November 2016:''' ''A small family of beta-xylosidases:'' The '''[[Glycoside Hydrolase Family 120]]''' page was completed and given [[Curator Approved]] status today by '''[[User:Spencer Williams|Spencer Williams]]'''.  '''[[Glycoside Hydrolase Family 120|GH120]]''' is currently a very small family, comprised of ca. 100 members originating exclusively from bacteria.  Following the initial identification of this family in 2011, enzymological and structural studies of two beta-xylosidases have revealed specifics of the catalytic mechanism ([[retaining]]) and an unusual beta-helix/beta-sandwich two-domain, tetrameric protein architecture.  Notably, the beta-helix domain resembles that of [[Polysaccharide Lyase Family 1]] and [[Glycoside Hydrolase Family 28]] members, and a complex structure with xylose revealed a large number of potential [[Surface Binding Site]]s.
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'''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!''
 
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'''16 November 2016:''' ''A new plant glycanase with a lysozyme fold:'' '''[[User:Spencer Williams|Spencer Williams]]''' does it again, with the completion of the '''[[Glycoside Hydrolase Family 134]]''' page on a new family of [[inverting]] beta-(gluco)mannanases.  This small family emerged in 2015 with the biochemical characterization of an ''Aspergillus nidulans'' (fungal) member.  Recently the tertiary structure and detailed catalytic mechanism - including the reaction [[conformational itinerary]] - of a ''Streptomyces'' sp. (bacterial) '''[[Glycoside Hydrolase Family 134|GH134]]''' member has been resolved by [[User:Gideon Davies|Gideon Davies]], [[User:Spencer Williams|Spencer Williams]], and their collaborators and co-workers.  This is only the second example of a [[glycoside hydrolase]] family that utilizes a lysozyme-like fold as a scaffold for the cleavge of a plant polysaccharide, as opposed to bacterial peptidoglycan; the first, a [[Glycoside Hydrolase Family 124]] cellulase characterized by [[User:Harry Gilbert|Harry Gilbert]] ''et al.'', also uses an [[inverting]] mechanism.
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'''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.''
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'''3 November 2016:''' ''New PDB links-out:'' For 3-D visualization of exemplar CAZymes and CBMs, we're trying a switch from [http://proteopedia.org/ Proteopedia] to the [https://doi.org/10.1093/nar/gkv402 NGL viewer] implementation at the RCSB Protein Data Bank.  We've made this switch site-wide across CAZypedia, and would like to [[Special:Contact|hear any feedback]] you might have. Here's an example for direct comparison: The seminal bacterial cellulose synthase complex [http://proteopedia.org/wiki/index.php/4hg6 in the JSMol viewer at Proteopedia] (including wiki page) and [http://www.rcsb.org/pdb/ngl/ngl.do?pdbid=4HG6 in the NGL viewer at the PDB] (other info available via the page tabs).
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'''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]]'''.
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'''30 October 2016:''' ''Another X-module comes to light:'' Today '''[[User:Spencer Williams|Spencer Williams]]''' completed the '''[[Glycoside Hydrolase Family 135]]''' page, which describes the genesis of a new CAZy family from a small group of modules formerly known as "X307" in the [[User:Bernard Henrissat|CAZyModO]] classification. The single biochemically and structurally characterized GH135 member hydrolyzes the unique fungal exo-polysaccharide galactosaminogalactan, with crystallographic evidence suggesting that the enzyme acts as a alpha-galactosaminidase.  However, a number of key enzymological questions about this new family remain outstanding, and we look forward to future work in this direction of the CAZyme landscape.
 
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'''3 September 2016:''' ''Galactosaminoglycan degradation:'' '''[[User:Spencer Williams|Spencer Williams]]''' has just completed a short entry on '''[[Glycoside Hydrolase Family 114]]''', a small family of bacterial and fungal sequences currently represented by a single characterized endo-alpha-1,4-polygalactosaminidase.  alpha-1,4-Polygalactosamine, also known as galactosaminoglycan, is produced as a secreted polysaccharide by select fungi, including Aspergilli.
 
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'''27 February 2016:''' ''The sweet side of sulfur:'' [[Author]] '''[[User:Spencer Williams|Spencer Williams]]''' has updated the '''[[Glycoside Hydrolase Family 31]]''' page to reflect the recent discovery of the first dedicated sulfoquinovosidases (SQases), previously ‘hidden’ within this family. SQases cleave α-glycosides of sulfoquinovose (6-sulfoglucose), which represent a significant reservoir of organosulfur in the biosphere. ''See the [[GH31]] page to discover more of the hidden charms of this family.''
 
 
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Latest revision as of 16:03, 21 November 2024

1 November 2024: Is this a world record? Six CAZypedia families in one fell swoop! The CBM47, CBM70, CBM96, CBM105, CBM106 and PL44 CAZypedia pages are now flipped to Curator Approved status. What do these diverse families from diverse origins with diverse binding specificities have in common? Astonishingly, at least one characterized member from each family interacts with a charged glycan! Wenwen Tao authored the CBM47, CBM96 and CBM106 pages, Menghui Sun authored the CBM70 page, Guanchen Liu authored the CBM105 page and Jinhang Zhou authored the PL44 page. All this under the responsible curatorship of Yaoguang Chang. Dive into these diverse families on their respective CAZypedia pages: CBM47, CBM70, CBM96, CBM105, CBM106 and PL44!

25 October 2024: Laminariawesome! Check out two new marine families of CBMs, CBM102 and CBM103, now on CAZypedia which have an ecological role in bacterial degradation of laminarin during phytoplankton blooms. Some function as surface glycan binding proteins but others have roles in targeting their appended catalytic modules to substrate. Both pages were authored by Marie-Katherin Zühlke. Read up on these environmentally important CBMs on their respective CBM102 and CBM103 pages!

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.

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