CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
 Totally new to the CAZy classification? Read this first.

Template:OlderNews

From CAZypedia
Revision as of 07:58, 17 May 2013 by Harry Brumer (talk | contribs)
Jump to navigation Jump to search

16 Jan 2013: Class I mannosidases × Williams2 = 90th CAZypedia GH page. Rohan Williams and Spencer Williams completed the Glycoside Hydrolase Family 47 page today to give CAZypedia its 90th Curator Approved GH page. GH47 is particularly important because it contains alpha-1,2 mannosidases that are responsible for N-glycan processing in eukaryotes. Delineated by subfamily membership, these eukaryotic mannosidases function either in glycoprotein maturation or endoplasmic reticulum-associated degradation (ERAD). Very few bacterial GH47 members are known, in contrast, and their function(s) has not been widely studied. From a mechanistic perspective, GH47 members are intriguing because the catalytic residues have not been unambiguously identified, despite high-resolution structure-function studies of these inverting enzymes. Check out the GH47 page to learn more!

14 Jan 2013: CAZypedia makes a contribution to MediaWiki community. We are proud to announce that BiblioPlus, an extension that provides automatic reference formatting to CAZypedia, has been officially accepted by the MediaWiki Extensions repository. BiblioPlus was coded by Karen Eddy, a UBC computer science student working with Harry Brumer, to resolve formatting issues with non-English characters in PubMed data. BiblioPlus is now available for anyone to use with any MediaWiki-based site to facilitate referencing journals and books. Thanks Karen, for all the hard work!

02 Dec 2012: Spencer does it again, twice. Spencer Williams has upgraded another two lexicon pages to Curator Approved status today. Have no idea what Oxazolinium ions and Oxocarbenium ions are, or why they're important in glycosidases? Check out these new pages!

20 Nov 2012: A growing lexicon, II: Spencer Williams has upgraded the Glycosyltransferases lexicon page to Curator Approved status today. This class of enzymes catalyzes the biosynthesis of the tremendous natural diversity of glycosides from activated sugar donor substrates and, as such, this page forms an essential part of CAZypedia's lexicon of terms and concepts. Thanks Spencer, for continuing to develop this resource!

16 Nov 2012: N-glycan deconstruction: There's been a flurry of activity on CAZypedia this past week; today, Al Boraston completed the Glycoside Hydrolase Family 125 page. GH125 was established last year based on a collaborative study between the Boraston and Vocadlo groups, which demonstrated that certain members from human bacterial pathogens can cleave alpha(1-6) mannosyl linkages typical of human N-glycans. Notably, GH125 members are also found in human gut symbiotic bacteria and pathogenic fungi, which underscores their potential biological importance in N-glycan deconstruction. Check out the GH125 page to read more about this new family, including a link to David and Al's seminal publication.

15 Nov 2012: A growing lexicon: Back in January of 2010, Wim Nerinckx compiled a monumental table on the orientation of the catalytic acid/base residue in over 70 GH families. Wim has now elaborated this page with an essential introduction to the important concept of Syn/anti lateral protonation in glycosidase catalysis, which was outlined in a seminal paper by Tom Heightman and Andrea Vasella in 1999. Now updated to Curator Approved from Under Construction status, this page forms a key part of CAZypedia's lexicon of terms and concepts.

12 Nov 2012: Three new GH families: Thanks to our colleagues in Japan, three pages on recently established glycoside hydrolase families have been completed and given Curator Approved status in CAZypedia today. The GH121 and GH127 family pages by Kiyotaka Fujita describe Bifidobacterium longum enzymes involved in plant hydroxyproline-rich glycoprotein (HRGP) deconstruction. The GH129 page by Hisashi Ashida describes another family of Bifidobacterial enzymes, which in this case, appear to be involved in mucin glycoprotein degradation. Special thanks go to Responsible Curator Shinya Fushinobu for organizing the production of these important new pages!

25 Oct 2012: A new GH family is born: Jean-Guy Berrin and his team at INRA in Marseille have recently unveiled a new glycoside hydrolase family, Glycoside Hydrolase Family 131, through elegant biochemical studies on a bi-modular β-glucanase from the fungus Podospora anserina. We are pleased to report that Jean-Guy has completed and given Curator Approved status to this fledgling CAZypedia page today, on which you can learn more about the INRA team's seminal work.

05 Sep 2012: Transglucosylases: The Glycoside Hydrolase Family 70 page by Magali Remaud-Simeon has been copy-edited by Responsible Curator Stefan Janecek and given Curator Approved status today. GH70 comprises a family of enzymes with the notable ability to build high molecular weight α-glucan polysaccharides from sucrose as a glucosyl donor substrate. Depending the particular enzyme, α-1,2-; α-1,3-; α-1,4-; and/or α-1,6-linked glucans can be produced, which have applications in food, pharmaceutical, and fine chemical industries. In addition, biofilms of α-1,3-glucans produced by the GH70 enzymes of oral bacteria are also implicated in the formation of dental caries (cavities). Learn more about this interesting family of CAZymes here!

21 Jun 2012: A new home! CAZypedia has physically moved a few thousand kilometers around the globe, and is now been served to you from the Michael Smith Laboratories at the University of British Columbia in Vancouver. In conjunction with the move, we are extremely happy to report that Karen Eddy, a summer project student at the MSL, has re-coded the buggy Biblio extension, so that now ALL literature references from PubMed are properly inserted into CAZypedia pages. Please do let us know if you experience any problems with CAZypedia following the move.

30 Apr 2012: A new cellulase fold: On April 27, Harry Gilbert completed the Glycoside Hydrolase Family 124 page here on CAZypedia. GH124 is a comparatively new, but tiny, family in the CAZy classification. This family is currently comprised of only three members (2 near-identical sequences from 2 Clostridium spp. and 1 from Ruminococcus albus), but was defined as a GH family based on the demonstration of cellulase activity in one of the Clostridial members. Remarkably, this enzyme was also shown to have a α8 superhelical fold, which has not been previously observed in cellulases, but is rather found in diverse lysozymes and lytic transglycosylases of GH23 active on bacterial cell wall peptidoglycan.

09 Mar 2012: β-glucuronidases!: Hot on the heels of their recent seminal structural and biochemical characterization of a Glycoside Hydrolase Family 79 β-glucuronidase, Hitomi Ichinose and Satoshi Kaneko have just completed the GH79 page in CAZypedia. GH79 is currently a rather small family comprised of enzymes from bacteria, fungi, plants, and mammals, which remove glucuronic acid (GlcA) or 4-O-methyl glucuronic acid from a diversity of substrates, ranging from secondary metabolites to structural biomolecules such as proteoglycans and arabinogalactan proteins. Click here to learn more about this interesting family!

11 Jan 2012: New for the new year: CAZypedia is proud to report that our first new page of 2012, the Glycoside Hydrolase Family 99 page, has been completed by Spencer Williams and given Curator Approved status today. This page follows the recent publication of seminal structural and mechanistic analyses by a multi-investigator team including CAZypedia Curators Spencer Williams and Gideon Davies, which suggests that endo-mannosidases of this family may use an unusual mechanism involving a 1,2-anhydro-β-mannopyranose ("sugar epoxide") intermediate to effect the release of Glc1–3-1,3-α-Man oligosaccharides during N-glycan trimming. GH99 is a small, but nonetheless important family, whose members come from both higher eukaryotes, which employ these enzymes in protein-folding quality-control, and bacteria, which are likely to use their homologues for carbohydrate scavenging in niche enviroments such as the human gut.

Also in the news: Spencer altered us to the fact that CAZypedia has clocked one million page views sometime recently. We're not quite sure what to make of that, but it seems like a pretty neat achievement. What is really interesting is that we are starting to see some dynamics in which pages are accessed most: Newer pages, such as GH18 (completed Oct. 2010), are becoming more popular than the very first CAZypedia page, GH1 (completed May 2007). And, some of the Lexicon pages, including those on the Cellulosome and anomeric configuration are right up there in the list. If you like to keep score, here's a list of our most popular pages. Want to find out when a particular CAZypedia page was Curator Approved? Click here.

18 July 2011: Our second GH-I chitosanase page: Ryszard Brzezinski has recently completed and Curator Approved his second page on chitosanases, enzymes which act specifically on the de-acetylated form of chitin (the polysaccharide chitin is a widespread in Nature as a main component of insect bodies and crustacean shells). Glycoside Hydrolase Family 80, a member of Clan GH-I together with GH24 and GH46, is a remarkably small family, which has thus far received only limited experimental attention. We therefore look forward to the expansion of this page with structural and mechanistic data in the future. Coincidentally, the GH80 page is our 80th Curator Approved Glycoside Hydrolase Family page in CAZypedia!

20 June 2011: More phosphorylases: On May 29, Author and Responsible Curator Hiroyuki Nakai completed the Glycoside Hydrolase Family 65 page. GH65 is comprised of alpha-glycoside phosphorylases and alpha,alpha-trehalose hydrolases. Due to the readily reversible nature of phosphorolysis, GH65 enzymes have been harnessed for glycoside synthesis, including recent work by Dr. Nakai. The completion of the GH65 complements previously completed pages on the beta-glycoside phosphorylases of GH94 and GH112 in CAZypedia.

12 May 2011: A new page on a new-ish family: Author and Responsible Curator Satoshi Kaneko completed the Glycoside Hydrolase Family 115 page today. GH115 contains microbial alpha-glucuronidases, which are involved the cleavage of D-glucuronic acid and 4-O-methyl-D-glucuronic acid sidechains from xylans. Remarkably, GH115 enzymes can release these monosaccharides from intact polymer chains, which is rather rare for exo-acting enzymes, and contrasts them with glucuronidases from GH67. Although this regiospecific activity has been known since the last millenium, it was only in 2009 that these particular enzymes nucleated their own GH family.

09 May 2011: It's a big news day here at CAZypedia. We are proud to announce that three distinct glycoside hydrolase family pages have been Curator Approved today:

We would like to express our sincere thanks to our Japanese and French colleagues for these important contributions to CAZypedia. Links to these families will be included in the next public update of the CAZy database (expected soon!).

Special thanks also go to Etienne for updating the Glycoside Hydrolase Family 82 page, including a very cool animated image that highlights enzyme domain movement during substrate binding - CAZypedia really is a living resource that can be continually improved with the latest knowledge.

28 April 2011: More on α-glucoside cleavage: Author and Responsible Curator Takashi Tonozuka recently completed the Glycoside Hydrolase Family 63 page, which has been updated to Curator Approved status today. GH63 is especially notable as it contains the eukaryotic "processing α-glucosidase I enzymes," which are essential for N-glycan trimming during glycoprotein maturation. Takashi Tonozuka's group has done seminal structural elucidation work in this family, and we very much appreciate his contribution to CAZypedia, especially during these tough times in Japan.

21 March 2011: A new page on the equinox (as we thaw-out and welcome the sun back to the Baltic region): Responsible Curator Anna Kulminskaya today approved the Glycoside Hydrolase Family 35 page, which was written by Anna, with input on the 3-D structure section from Mirko Maksimainen and Juha Rouvinen. GH35 is a family of β-galactosidases from diverse organisms that display a range of bond specificities. Only very few tertiary structures have been solved in this family, to which the Russian and Finnish groups have made seminal contributions.

28 February 2011: Hexosaminidases!: The Glycoside Hydrolase Family 20 and Glycoside Hydrolase Family 84 pages, which were completed last week by Author Ian Greig and approved by Responsible Curator David Vocadlo, have today been cross-linked from the CAZy database (look out for the next public release). GH20 is of significant medical relevance, as it contains the human enzymes HexA and HexB, deficiencies of which case Tay-Sachs disease and Sandhoff diseases, respectively. GH84 is similarly important in the context of cell and organism biology, as this family contains human OGA (HexC, MGEA5, O-GlcNAcase), a nuclear and cytoplasmic enzyme that is responsible for dynamic modulation of β-linked O-GlcNAc residues linked to serine and threonine residues. O-GlcNAc'ylation of specific protein residues has in some cases been found to be reciprocal to phosphorylation and, accordingly, has implicated O-GlcNAc in diverse cellular processes and disease states.

07 February 2011: A landmark CAZypedia page: This one has been a long time coming, but today Birte Svensson and Stefan Janecek completed the Glycoside Hydrolase Family 13 page. GH13 is, quite simply, THE family of α-glucoside-degrading and -rearranging enzymes, with over 10000 members distributed into more than 35 subfamilies, which represent tens of enzyme activities. Due to the central role starch (amylose/amylopectin) and glycogen play in energy storage, these enzymes are of immense ecological and biotechnological importance. GH13 is also our 70th Curator Approved GH Family page!!!

17 January 2011: Our first news for the new year: Peter Reilly has just completed and approved the Glycoside Hydrolase Family 44 page. GH44 is another classic cellulase family (formerly known as cellulase family J); a number of these endo-beta(1-4)-glucanases have a penchant for degrading xyloglucan as well as soluble synthetic cellulose derivatives.

29 October 2010: News from sunny Provence: Florence Vincent has completed the Glycoside Hydrolase Family 73 page, which has just been edited and approved by Senior Curator Bernard Henrissat. GH73 contains peptidoglycan hydrolases with endo-β-N-acetylglucosaminidase (NAG, a.k.a. GlcNAc) specificity. Mechanistic and structural parallels between this family and other hexosaminidase families have been drawn, including GH18, whose CAZypedia page was very recently finished (see the preceding News item from Oct. 13).

13 October 2010: Gideon Davies has just completed and approved the Glycoside Hydrolase Family 18 chitinase/endo-β-N-acetylglucosaminidase page, with help from Nathalie Juge on the non-catalytic proteins in the family, which function as carbohydrate-binding proteins or enzyme inhibitors. Look out for links to this and several of the pages mentioned in previous News items in the latest version of the CAZy database, to be released today!

08 October 2010: Trehalases!: CAZypedia Author Tracey Gloster completed the Glycoside Hydrolase Family 37 page today, which was summarily approved by Responsible Curator Gideon Davies. GH37 is a trehalase-specific family; trehalases are also currently found in GH15 and GH65.

06 October 2010: A hat-trick: Glycoside Hydrolase Family 5 makes three Curator Approved family pages by Gideon Davies in one day. GH5 is a large, poly-specific family, which makes covering the entire scope of this family challenging. CAZypedia is an evolving resource, so readers are welcome to suggest further improvements.

06 October 2010: More cellulases - the second family from Gideon in one day: The Glycoside Hydrolase Family 45 page has been completed and approved by Senior Curator Gideon Davies. GH45 contains endo-β(1-4)glucanases (endo-cellulases), and a significant structural similarity to plant expansins has been observed.

06 October 2010: Yet another classic cellulase family: The Glycoside Hydrolase Family 6 page by Kathleen Piens and Gideon Davies has just been upgraded to Curator Approved status. GH6 contains cellobiohydrolase II (CBHII, or Cel6A in the modern nomenclature), which is a main component of the enzyme cocktail secreted by the proficient cellulose-degrading organism, Hypocrea jecorica (née Trichoderma reesei).

24 August 2010: Another classic cellulase family: David Wilson and Breeanna Urbanowicz have teamed-up to produce the Glycoside Hydrolase Family 9 page, which has been upgraded to Curator Approved status today. GH9 is a family of inverting endo-beta(1-4)glucanases with a long history, including important structure/function work from David's lab. Bree has written a special addendum on the structure, function, and phylogeny of the plant endoglucanases, which have been implicated in cell wall biosynthesis.

11 August 2010: A new look. Today we upgraded the MediaWiki software that runs CAZypedia and switched the default interface to the shiny new Vector skin, which you may have already noticed on Wikipedia. Let us know if you find any problems with the new layout here. (If preferred, CAZypedians can actually still use the old default skin, Monobook, by logging in and changing their user preferences.)

10 August 2010: A bit of extra polishing: Curator and Author Harry Gilbert has now touched-up and further improved the Glycoside Hydrolase Family 43 α-L-arabinofuranosidase/β-D-xylosidase page, which was Curator Approved back in November 2009.

22 July 2010: Number 60! Today CAZypedia chalks-up its 60th Curator Approved Glycoside Hydrolase Family family page, GH116 by Author Beatrice Cobucci-Ponzano and Responsible Curator Marco Moracci. GH116 is a brand-new beta-glycosidase family, which was created after a seminal publication by the Neapolitan group in The Journal of Biological Chemistry very recently (in print July 2...check the GH116 page for more details!).

8 July 2010: CAZypedia breaks new ground: CAZypedia has made its first foray into the world of glycosyltransferases with the GT42 page by Warren Wakarchuk. The Glycosyltransferase Families are still very much in a beta test stage, and we welcome input and ideas on the format of these pages.

30 June 2010: Mirjam does it again: Responsible Curator Mirjam Czjzek has just finished-off the Glycoside Hydrolase Family 50 beta-agarase page. GH50 is a family in Clan GH-A, so although not much has been experimentally determined in this family (thus making it a rather small page), a lot can be inferred. Mirjam is in charge of 4 GH pages right now, and GH50 is the third she and her co-authors have completed to-date. Thanks Mirjam!

29 June 2010: A classic cellulase family: The Glycoside Hydrolase Family 7 page by Jerry Ståhlberg, which has been essentially complete for some time now, has recently been upgraded Curator Approved status; a link from the CAZy DB will soon follow. Notably, GH7 contains classic cellobiohydrolases and endo-glucanases, which are the focus of much attention these days for the saccharification of cellulose for biofuels.

21 June 2010: Complexes for degrading a complex substrate: We are happy to report (from the home of the Swedish biorefining, no less) that Bareket Dassa, Orly Alber, and Ed Bayer have just finished the Cellulosome page in the Lexicon. Ed pioneered Cellulosome research, so this overview and historical summary is a really significant contribution to CAZypedia.

27 May 2010: A new lysozyme page: The GH25 page by Ed Taylor has recently been Curator Approved by Gideon Davies and is now linked from the CAZy database.

25 May 2010:

Thumb up icon 62px.png

We have finally fixed the problem with non-English characters in references from PubMed that was breaking some pages! We apologize for the delay and any inconvenience this may have caused.

18 May 2010: New from 日本: Curator Takashi Tonozuka has just completed and approved his page on the dextranase/pullulanase family GH49. Thanks go to Takashi for finishing the page despite our our ongoing troubles with PubMed references!

10 May 2010: Curator Yuval Shoham has just completed the Glycoside Hydrolase Family 51 page. GH51 is primarily an α-L-arabinofuranosidase family, whose members - like some GH43 enzymes - are involved in trimming the sidechains from plant xylans. These enzymes are therefore of potential interest in biomass processing.

27 April 2010: More from Marseille: Senior Curator Bernard Henrissat has edited and Curator Approved the Glycoside Hydrolase Family 17 page written by Geoff Fincher. GH17 contains a variety of endo-acting beta-1,3-glucanases and mixed-linkage glucanases. Notably, nearly all of the enzymologically characterized members to-date are from plants. Expect a link from the CAZy DB soon...

16 April 2010: This just in via our news desk in Marseille: Vincent Eijsink has just finished and given Curator Approved status to our first chitinase page, Glycoside Hydrolase Family 19, following on the heels of the GH46 chitosanase page completed in February. Vincent has included some very nice structure figures on the GH19 page, which add a nice splash of color and clarity.

7 March 2010: We are proud to announce that all four pages Curated by Anthony Clarke on peptidoglycan-degrading families have been Curator Approved and further improved over the past couple of weeks. So, in addition to GH23, which made the news on Feb. 18, CAZypedia now contains completed pages on GH102, GH103 and GH104!

19 February 2010: It's been a busy week here at CAZypedia: Tirso Pons and Wim Van den Ende just finished the Glycoside Hydrolase Family 68 page, which makes four new Curator Approved pages in four consecutive days!

18 February 2010: O Canada! Anthony Clarke of the University of Guelph approved the Glycoside Hydrolase Family 23 page today, which is the first of four pages that he's agreed to curate on peptidoglycan-degrading enzymes. Look out for more from Anthony on CAZypedia in the near future...

17 February 2010: The page on the tiny iota-carrageenase family Glycoside Hydrolase Family 82 (containing only 2 members!) has been given Curator Approved status by Gurvan Michel and Mirjam Czjzek from Roscoff, Bretagne.

16 February 2010: Dr. Bareket Dassa and Prof. Ed Bayer have just finished and given the Curator Approved stamp to the Glycoside Hydrolase Family 48 page. For the old-timers out there, GH48 used to be called "Cellulase Family L".

10 February 2010: In our 2nd news flash of the day, Ryszard Brzezinski has completed work on the chitosanase family page, Glycoside Hydrolase Family 46. This new entry brings the total number of Curator Approved Glycoside Hydrolase Family pages to 44!

10 February 2010: Leila Lo Leggio has completed and given Curator Approved status to the Glycoside Hydrolase Family 53 page today. GH53 enzymes are involved in plant biomass conversion through the degradation of beta-1,4-galactan, and Leila has been involved in a number of key structural studies of these enzymes.

22 January 2010: David Rose has just updated the references on the GH38 page with some recently published work on the role of cations in the active site, which gives us a good excuse to showcase this page (finished back in August 2009) here in the Latest News section. GH38 contains the Class II Golgi and lysosomal α-mannosidases involved in N-glycan processing on which David has done a lot of pioneering structural work. Thanks David!

19 January 2010: Glycoside Hydrolase Family 58, which contains the E. coli bacteriophage tailspike endo-sialidases, has now been given Curator Approved status by author and curator Warren Wakarchuk. This is the second page by Warren, who did GH101 back in the autumn of 2009.

16 January 2010: Gerlind Sulzenbacher has completed a CAZypedia page on the α-L-fucosidase family GH29, which has just been approved by Responsible Curator Steve Withers. GH29 is particularly notable as it contains human α-fucosidase A1 (FucA1), defects in which give rise to the lysosomal storage disease fucosidosis.

15 January 2010: The Glycoside Hydrolase Family 57 has now been finished and given "Curator Approved" status by Stefan Janecek. This is CAZypedia's second page on starch-active enzymes, following Pedro Coutinho's GH15 contribution (see News, Nov. 6, 2009).

12 January 2010: Wim Nerinckx has just completed the herculean task of compiling an updated table on the orientation of the catalytic acid/base residue (syn vs. anti protonation) in all GH families, where known. Look out for a full lexicon entry by Wim and Spencer Williams soon!

11 January 2010: CAZypedia proudly announces our second page of the new year: Mirjam Czjzek (Station Biologique de Roscoff, France) and Wim Van den Ende (KULeuven, Belgium) have just completed the Glycoside Hydrolase Family 32 page!

04 January 2010: CAZypedia proudly announces our first page of the new year: Glycoside Hydrolase Family 92 by Prof. Harry Gilbert, which is based on work very recently published in Nature Chemical Biology.

06 November 2009: The glucoamylase family GH15 now has a completed draft in place, courtesy of Pedro Coutinho (yep, that Pedro...). Expect a link from CAZy DB soon!

03 November 2009: Thanks to Marco Moracci, the GH42 page is now ready!

28 October 2009: Continuing the flurry of recent activity, curator Al Boraston has approved the GH85 and GH98 pages written by Wade Abbott and Fathima Aidha Shaikh, respectively. GH55, GH67, GH85, and GH98 are all now cross-linked with the Oct. 28 version of the CAZy database, thanks to Bernie.

27 October 2009: The GH55 page is now in place, written by Takuya Ishida and Kiyohiko Igarashi, and curated by Shinya Fushinobu.

26 October 2009: Harry Gilbert has just finished the Glycoside Hydrolase Family 67 page!

15 October 2009: 24 Glycoside Hydrolase Families have now been completed in CAZypedia and are linked from their respective pages in latest release of the CAZy Database.

5 October 2009: Tracey Gloster (author) and Gideon Davies (curator) have finished work on the Glycoside Hydrolase Family 97 page, which is now ready for public viewing.

Retrieved from "http://www.cazypedia.org/index.php?title=Template:OlderNews&oldid=8683"