New to the CAZy classification? Read this first.
Want to learn more about CAZypedia? Read the CAZypedia 10th anniversary article in Glycobiology.
Difference between revisions of "News"
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Revision as of 05:17, 7 March 2010
This page is a simple compilation of all the blurbs that have appeared in the "Latest news" section of the CAZypedia Main Page.
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.
14 February 2020: A rose by any other name would smell as sweet. The human gut bacterium Roseburia intestinalis provides a Curator Approved Carbohydrate Binding Module Family 86 page as a special Valentine Day's gift. CBM86 members are structurally located at the N-termini of GH10 xylanase polypeptides. Roseburia intestinalis certainly enjoys the sugary xylans it encounters in the dietary tract as a carbon source and likely uses the CBM86 modules to enhance xylan capture through improved xylan affinity for the xylanase enzymes. The CBM86 page was written in record time by Maria Louise Leth with Maher Abou Hachem acting as Responsible Curator. Read more about this 'rosy' xylan-binding family here.
16 December 2019: Closing the year with marine CAZymes: The Glycoside Hydrolase Family 107 page, which describes a family of endo-1,4-fucanases, was finalized today by Author David Teze and Responsible Curator Alisdair Boraston. The characterized enzymes of this family hydrolyze the marine polysaccharides known as fucoidans (sulfated fucans). First identified by the Roscoff group in 2006 (see e.g. Gurvan Michel and Mirjam Czjzek), recent collaborative work by the Withers and Boraston groups has resolved the structure and mechanism of GH107. Of particular note, crystallography of two GH107 members has revealed similarity with GH29 members, which together now form the new Clan GH-R. See the GH107 page for the details from the seminal publications on this family!
Friday the 13th of December 2019: A spooky Christmas gift: The bacterial CBM71 family is a new addition to CAZypedia CBM just in time for Christmas! The CAZypedia CBM page describes the characterization of two lactose- and lacNAc- binding Pneumococcal CBM71 members. The page was authored by Ben Pluvinage with Alisdair Boraston acting as responsible curator. Find out more on the CBM71 family here!
3 November 2019: Xylan-cleaving LPMOs: Today, Responsible Curator Jean-Guy Berrin approved the Auxiliary Activity Family 14 page authored by Marie Couturier, which describes one of the newer families of lytic polysaccharide monooxygenases (LPMOs) described in the CAZy database. AA14 was first described in 2018 by Marie, Jean-Guy, and their co-workers. Notably, they showed that the founding members of this family were specific for the plant cell wall matrix glycan, xylan, which contrasts other families of LPMOs that are predominantly cellulose- or chitin-active. Check out the AA14 page for more details!
24 October 2019: A tale of an amoebal CBM: The Carbohydrate Binding Module Family 55 page discussing the pathogenically interesting chitin-binding CBM55 family has been flipped to curator approved. The CBM55 family was first identified from Entamoeba histolytica, a protist that causes dysentery and liver abscesses. The page was authored by John Samuelson with Elizabeth Ficko-Blean acting as responsible curator. Read more on this amoebal CBM family on the CBM55 page.
15 October 2019: A new debut for beta(1-2): The Glycoside Hydrolase Family 144 page, which describes the β-1,2-glucanases in this family, was completed by Author Koichi Abe and Responsible Curator Masahiro Nakajima today. GH144 was founded in 2017 based on a seminal publication by Koichi Abe, Masahiro Nakajima, and their colleagues. Interestingly, GH144 contains both endo-β-1,2-glucanases (EC 126.96.36.199), as well as exo-acting enzymes that release sophorose (Glc-β(1,2)-Glc) from the nonreducing end of β(1,2)-glucan chains ("sophorohydrolases", analogous to the more well-known "cellobiohydrolases") Learn more about these enzymes, whose protein structure is distantly related to that of the fungal β-1,2-glucanases from GH162, on the GH144 page!
1 August 2019: Sweet Sixteen: The Carbohydrate Binding Module Family 16 page in CAZypedia has been flipped to Curator Approved today. The page features CBM16 members from two environmental bacteria with very different backgrounds: One bacterium was isolated from a red alga (red seaweed) and its GH16 kappa-carrageenase-appended CBM16 binds the red algal extracellular matrix polysaccharide carrageenan and influences the processive mechanism of the catalytic module. The other bacterium was isolated from organic waste leachate and deletion of both its CBM16s from a GH5 mannanase severely impairs binding ability of the catalytic module. The CBM16 page was Authored by Maria Matard-Mann with Elizabeth Ficko-Blean acting as Responsible Curator. Learn more about these "sweet sixteen" CBMs on the CBM16 page.
21 July 2019: Back to the future: Author James Stevenson and Responsible Curator Joel Weadge completed the Glycoside Hydrolase Family 105 page today, which is related to the recently completed (see below) GH88 page. Like GH88, GH105 comprises hexeuronic acid hydrolases that use a distinct mechanism of glycosidic bond cleavage. You can learn more about these enzymes on the GH105 and GH88 pages. We'd like to especially thank Joel and James for taking the initiative to reach out on their own to offer to produce the GH105 page; this is directly in the spirit of CAZypedia as a community-led, volunteer resource!
17 July 2019: A flashback on unsaturated glucuronyl hydrolases: Back in 2015, Author Seino Jongkees essentially completed the Glycoside Hydrolase Family 88 page, which was finally upgraded to Curator Approved status today. GH88 unsaturated glucuronyl hydrolases use an atypical glycoside hydrolase mechanism that involves the hydration of the double bond between carbons 4 and 5 of the non-reducing terminal sugar of their substrates and subsequent rearrangement. In this way, the activity of GH88 enzymes is dependent on the prior action of Polysaccharide Lyases to produce the required hexenuronic acid terminus. Learn more about these non-canonical enzymes, and their cousins in GH105, on the GH88 page.
15 July 2019: Of carbohydrates, esters, and lignin: Authors Jenny Arnling Bååth and Scott Mazurkewich, together with Responsible Curator Johan Larsbrink finalized CAZypedia's third Carbohydrate Esterase Family page today. Carbohydrate Esterase Family 15 comprises glucuronoyl esterases that utilize a classical serine hydrolase catalytic triad to cleave pendant non-carbohydrate groups from, for example, plant glucuronoxylan (i.e. de-esterification with the sugar as the acid). CE15 members have therefore be suggested to facilitate the breakdown of lignin-carbohydrate complexes (LCC) and are of growing interest for biomass processing. Learn more about these enzymes, including the seminal work of Peter Biely and colleagues, on the CE15 page.
5 June 2019: New and cool beta(1,2)-glucanases of GH162: Today Author Nobukiyo Tanaka and Responsible Curator Masahiro Nakajima completed the Glycoside Hydrolase Family 162 page in CAZypedia. As its high number would imply, GH162 is one of the newest families in the CAZy classification, of which the first example has been elegantly characterized in 2019 by Drs. Tanaka and Nakajima and their colleagues. GH162 is a tiny family of mostly fungal members, which has structural and mechanistic commonality with GH144, and may be distantly related to GH8 (Clan GH-M) and GH15 (Clan GH-L). Learn more about all of these families on their respective pages.
14 May 2019: Starch... it's not over yet: Two new families of starch-binding CBMs, CBM82 and CBM83, have joined the CAZypedia ranks. These CBMs are both found in an enormous multi-modular cell-wall anchored enzyme from a gut bacterium. The pages were both authored by Darrell Cockburn with Nicole Koropatkin acting as responsible curator. Learn more about the new starch-binding CBM82 and CBM83 families on their respective pages.
28 February 2019: CE9 is CE page #2!: Graduate student Alex Anderson has completed CAZypedia's second Carbohydrate Esterase (CE) family page, Carbohydrate Esterase Family 9, which was Curator Approved by his supervisor Michael Suits today. CE9 enzymes are metal-dependent N-acetylglucosamine 6-phosphate deacetylases that function in peptidoglycan recycling in bacteria. CE9 is a huge family, currently comprising over 10,000 members (nearly all are from bacteria), which underscores their biological importance. Alex and Mike completed CAZypedia's first CE family page, CE4 earlier this month, and we thank them for these seminal expansions of of our resource. Learn more about the structure and mechanism of metal-dependent deamidases here: CE9, CE4.
22 February 2019: Starch-active LPMOs: Glyn Hemsworth recently completed the Auxiliary Activity Family 13 page, which was Curator Approved by Responsible Curator Gideon Davies today. AA13 was first identified in 2014 and is notable as the first lytic polysaccharide mono-oxygenase (LPMO) family that is active on alpha-glycosidic bonds, viz. those in amylose (starch). Overall, LPMOs are an intriguing group of copper-dependent oxidases that open-up insoluble polysaccharide substrates for increased attack by glycoside hydrolases. Read more about AA13 and related beta-glycan-active LPMOs (AA9, AA10, AA11, AA14, & AA15) on their respective CAZypedia pages and at the CAZy Database.
4 February 2019: CAZypedia's first CE page! Today Responsible Curator Michael Suits approved the Carbohydrate Esterase Family 4 page authored by graduate student Alex Anderson, thereby marking a new milestone CAZypedia's history. Carbohydrate Esterases (CEs) catalyze the de-O-acylation or de-N-acylation of saccharides (the latter are formally amidases), and CE4 contains members with either activity, e.g. acetylxylan esterases and peptidoglycan deacetylases. CE4 members thus play diverse biological roles in nature. Learn more about the structure and mechanism of these metal-dependent de-acylases here.
27 November 2018: Remember, remember... an end of November new CAZypedia CBM family page. The type C L-rhamnose binding CBM67 family is now on-line in CAZypedia. Satoshi Kaneko authored the page and Harry Gilbert acted as responsible curator. Learn more about the structure and function of the CBM67 family on its CAZypedia page.
23 November 2018: Welcome to the CAZypedia fold CBM49! The crystalline cellulose-binding CBM49 CAZypedia page was authored by Breeanna Urbanowicz and Elizabeth Ficko-Blean. Breeanna Urbanowicz also acted as responsible curator. There is experimental evidence that rice CBM49 is cleaved post-translationally in vivo which probably plays an important role in plant growth. Find out more about the functionally interesting family 49 CBMs here.
11 October 2018: Fall ushers in a new CAZypedia CBM family page. The chitin-binding and lytic polysaccharide monooxygenase associated CBM73 family is described in detail. Zarah Forsberg authored the page and Gustav Vaaje-Kolstad acted as responsible curator. Learn more about the CBM73 family on its CAZypedia page.
24 September 2018: Revenge of the Ruminococci Part Deux. Two more CBM families from Ruminococcal bacteria are ready for reading. The CBM79 and CBM80 CAZypedia pages were authored by Immacolata Venditto and Harry Gilbert acted as responsible curator. These CBMs are important for enzyme targeting but also for targeting the entire cellulosome complex to substrate. More information on the CBM79 and CBM80 families can be found on their respective CAZypedia pages.
3 July 2018: Revenge of the Ruminococci. Three CBM families containing characterized CBM members from Ruminococcal bacteria are now on-line in CAZypedia; two of these families contain uniquely Ruminococcal CBMs. Ana Luis authored the pages (in one fell swoop) and Harry Gilbert acted as responsible curator. Descriptions of families CBM75, CBM76 and CBM77 can be found on their respective CAZypedia pages.
4 June 2018: When two worlds collide. The CBM81 family has an interesting binding mechanism, mixing characteristics of both type A and type B CBMs. The binding is enthalpically driven to soluble ligands, so by definition this is a type B interaction; however, the CBM binding face resembles the flat face of type A (crystalline-polysaccharide binding) CBMs. Marcelo Liberato authored the CBM81 page and Fabio Squina acted as the Responsible Curator. Find out more about the unusual family 81 CBMs here.
25 May 2018: The almost exclusive expansin associated CBM63 family is on-line. An interesting function is described as a bacterial CBM63 targets expansin to biomechanical hotspots in the Arabidopsis cell wall, where cell wall loosening occurs. The page was authored by Will Chase and Daniel Cosgrove with Daniel Cosgrove acting as responsible curator. Learn more about this expansin family CBM here.
4 May 2018: CAZypedia's first non-LPMO Auxiliary Activity Family page! Today Responsible Curator Roland Ludwig approved Daniel Kracher's and his expansive Auxiliary Activity Family 3 page. AA3 comprises a number of FAD-dependent redox enzymes including cellobiose dehydrogenase, aryl alcohol oxidase/dehydrogenases, glucose oxidases and glucose dehydrogenases, pyranose dehydrogenase, alcohol oxidase, and pyranose oxidase across four subfamilies. Roland and Daniel have done a monumental job in succinctly capturing the diversity of this family, which you can read about here.
2 May 2018: The CBM65 page has been added to the CAZypedia fold. This is a small CAZy family with two currently characterized members from an anaerobic cellulolytic ruminal bacterium. The two CBM65 members bind various beta-glucans and play an important role in enhancing enzymatic activity on substrate. The page was authored by Ana Luis and Harry Gilbert acted as responsible curator. Learn more about this CBM family here.
1 March 2018: The shortest month of the year saw four CBM families reach Curator Approved status, including two early members. Harry Gilbert with input from Ed Bayer, who also acted as Responsible Curator, authored the cellulose-binding CBM3 page. Harry Gilbert and Claire Dumon both contributed to the xylan and glucan-binding CBM4 page. The xylan-binding CBM22 page was taken on by Harry Gilbert solo. Finally, the cellulose-binding CBM78 family was authored by Immacolata Venditto, with Harry Gilbert acting as Responsible Curator. Learn more about each of these families on their respective pages.
15 February 2018: More on pectin, and also arabinan: Jonathon Briggs recently completed the Glycoside Hydrolase Family 147 and Glycoside Hydrolase Family 146 pages, which are involved in the utilization of pectin and galactan, respectively, by human gut Bacteroidetes. Both pages were upgraded to Curator Approved status today by Responsible Curator Harry Gilbert. Learn more about these newly described families at GH146 and GH147.
13 February 2018: The intricacies of pectin deconstruction: Rhamnogalacturonan II (RGII) represents the most structurally complex plant cell wall polysaccharide currently known, the complete saccharification of which requires a battery of CAZymes. Under the guidance of Responsible Curator Harry Gilbert, four new GH pages related to RGII deconstruction were Curator Approved today. Special thanks go to Authors Ana Luis (GH106, GH139, and GH141) and Didier Ndeh (GH138) for their hard work in putting these pages together. Learn more about the individual, specific contributions of each of these families (three of which have been recently uncovered) to microbial RGII utilization on their respective pages.
31 January 2018: A flurry of CBM activity in the new year: Over the past two weeks, CAZypedia has enjoyed the promotion of no less than nine(!) Carbohydrate-binding module (CBM) family pages to Curator Approved status, thanks to the tenacity of CBM vanguard Harry Gilbert and the keen editorial oversight of Elizabeth Ficko-Blean. In order of appearance, CBM2, CBM10, CBM15, CBM29, CBM66, CBM60 (co-authored by Cedric Montanier), CBM46, and CBM35 all have completed pages, as does the deleted family CBM7. These pages cover many classic CBM studies and include examples of type A, type B, and type C CBMs. The CBM legacy runs deep - learn more about each family on their respective pages.
20 January 2018: A seminal LPMO family: Vincent Eijsink and Gustav Vaaje-Kolstad today completed the Auxiliary Activity Family 10 page. Work from the Norwegian group was seminal in defining the action lytic polysaccharide mono-oxygenases as a new paradigm in chitin cleavage, ultimately leading to the reclassification of CBM33 as AA10. This work was also influential in the reclassificaiton of GH61 to AA9. Read more about the exciting history of these exciting enzymes on their respective pages.
26 November 2017: CBM #1: Today, CBM pioneer Markus Linder completed the Carbohydrate Binding Module Family 1 page. CBM1 comprises the canonical fungal cellulose-binding modules (originally known as cellulose-binding domains), which were first found as stable cystine-knot-containing protein fragments released by controlled proteolysis of cellulases. The planar nature of the substrate-binding face, and linear arrangement of key aromatic residues, represent the archetype of CBMs that mediate glycosidase targeting to crystalline polysaccharides. Building on the original discovery of the modules now classified into CBM1 in Sweden, Markus Linder (then a Ph.D. student) and Tuula Teeri, working together across the Baltic Sea in Finland, were among the first to undertake structure-function studies and protein engineering of CBM1 using modern molecular techniques in the mid- to late-1990s. We're pleased to finally have this one in CAZYpedia - learn more about this seminal CBM family here.
11 October 2017: Ten years of CAZypedia! We are proud to announce the publication of a new article in Glycobiology in celebration of CAZypedia's tenth anniversary online. This article was written on behalf of all of present and future Contributors by Curators Harry Brumer and Spencer Williams, with input from a number of key individuals involved in the genesis of CAZypedia (see the Acknowledgements section for full details). A post-print version of the manuscript will be freely available from the UBC Library Open Collections, in addition to the final version on the Glycobiology website. Thanks to the hard work of a multitude of Contributors, CAZypedia is a successful example of community-driven, expert-based biocuration. We look forward to the continued development of this resource over the next ten years - and beyond!
10 September 2017: Sussing-out starch recognition in CBM58. We are excited to report that Nicole Koropatkin has completed the Carbohydrate Binding Module Family 58 page today. CBM58 constitutes a comparatively small family of CBMs found in bacteria in the phylum Bacteroidetes, including key members of the human gut microbiota such as Bacteroides thetaiotaomicron. Within these bacteria, CBM58 modules are found inserted within the GH13 catalytic module of SusG, the essential outer-membrane-bound amylase of the starch utilization system (sus). Nicole’s seminal structural biology has defined the family and provided insight into the recognition of amylose helices by CBM58 members in SusG homologs. Read more about this fascinating system here.
10 April 2017: A classic GH family. The Glycoside Hydrolase Family 22 page was completed today by Spencer Williams, with editorial input from Responsible Curator David Vocadlo. GH22 contains the classic bacterial peptidoglycan hydrolase, hen egg-white lysozyme (HEWL), the first enzyme for which the three-dimensional structure was solved (reported in 1965). Moreover, seminal enzyme-carbohydrate complex structures have made HEWL a paradigm for glycosidases that operate through the classical Koshland retaining mechanism. Although the nature of the reaction intermediate remained contentious for many years since the original proposal of an oxacarbenium ion-carboxylate pair, a definitive study by Vocadlo, Davies, Laine, and Withers resolved the covalent nature of the glycosyl-enzyme HEWL in 2001, thus bringing mechanistic understanding of this classic enzyme in concordance with other retaining GH families. The lysozyme fold of HEWL defines the archetype for other hexosaminidases (i.e. those of GH19 and GH23) and the non-catalytic alpha-lactalbumins, and this fold notably has also been observed in recently emergent families of cellulases (GH124) and mannanases (GH134). Find out more about this classic GH family here!
2 December 2016: A new CAZyme-specific journal. The journal Amylase has been recently launched under the editorial leadership of Stefan Janecek and a number of other CAZypedians, including Bernard Henrissat, Magali Remaud-Simeon, Birte Svensson, Pedro Coutinho, and Leila LoLeggio. 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 Amylase homepage for more information on the scope of the journal and details on how to submit manuscripts for publication.
29 November 2016: A small family of beta-xylosidases. The Glycoside Hydrolase Family 120 page was completed and given Curator Approved status today by Spencer Williams. 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 Sites.
16 November 2016: A new plant glycanase with a lysozyme fold. 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) GH134 member has been resolved by Gideon Davies, 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 Harry Gilbert et al., also uses an inverting mechanism.
3 November 2016: New PDB links-out. For 3-D visualization of exemplar CAZymes and CBMs, we're trying a switch from Proteopedia to the NGL viewer implementation at the RCSB Protein Data Bank. We've made this switch site-wide across CAZypedia, and would like to hear any feedback you might have. Here's an example for direct comparison: The seminal bacterial cellulose synthase complex in the JSMol viewer at Proteopedia (including wiki page) and in the NGL viewer at the PDB (other info available via the page tabs).
30 October 2016: Another X-module comes to light. Today 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 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.
3 September 2016: Galactosaminoglycan degradation. 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.
27 February 2016: The sweet side of sulfur. Author 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.
11 September 2015: Let's hear it for the transglycosylases! Today, Authors Ramon Hurtado-Guerrero and Thierry Fontaine, together with Responsible Curator Bernard Henrissat, completed the Glycoside Hydrolase Family 72 page. GH72 is a small but important family of beta(1-3)-glucan transglycosylases that function to remodel the cell wall during the growth of yeast and other fungi. Predominant or strict transglycosylases are relatively rare in GH families, with other notable examples coming from GH13, GH16, GH31, GH70, and GH77. Read more about GH72 and what makes transglycosylases so interesting here in CAZypedia!
6 August 2015: Live from the Cellulase/CAZyme GRC. CAZypedia marches on with the completion of the Polysaccharide Lyase Family 1 today by Responsible Curator and Author Richard Pickersgill, with additional editing by Polysaccharide Lyase Families coordinator Wade Abbott. PL1 contains pectate lyases from microbes and plants, which are key enzymes in plant cell wall remodelling/break-down. The solution of the crystal structure of a pectate lyase C from the plant pathogen Erwinia chrysanthemi was the first to reveal the parallel beta-helix as a novel protein fold that is now known to serve as the scaffold of other pectinolytic enzymes, including pectin hydrolases (GH28) and pectin methylesterases (CE8). Read more about the discovery of pectate lyases and the enzymology and crystallography of PL1 here.
28 July 2015: 100 GH FAMILIES!!! We are extremely pleased to announce that CAZypedia has reached the key milestone of 100 Curator Approved Glycoside Hydrolase Family pages today, thanks to the completion of the Glycoside Hydrolase Family 12 page by Gerlind Sulzenbacher. GH12 is one of the classic "cellulase" families (formerly known as cellulase family H) defined early in the history of the CAZy classification; GH12 is now known to comprise both microbial endo-glucanases and endo-xyloglucanases. The completion of this page is especially timely in advance of the upcoming 2015 GRC on Cellulosomes, Cellulases & Other Carbohydrate Modifying Enzymes, happening next week. Gerlind performed the seminal crystallography in this family (under the mentorship of Gideon Davies), and we would especially like to thank her for producing an excellent summary and series of figures for the "Three-dimensional structures" section.
The Board of Curators would also like to take the opportunity of this key milestone to express our sincere gratitude to our many expert Contributors for their time and dedication to building CAZypedia as a community-based resource over the past 8 years. In addition to the 100 Curator Approved GH pages, CAZypedia also currently contains 5 PL Family pages, 2 AA Family pages, 2 GT Family pages, 10 CBM Family pages, and 22 Lexicon pages!
19 March 2015: Closing-in on 100. CAZypedia is on the way to an important milestone, our 100th Curator Approved Glycoside Hydrolase Family page. Thanks go to our colleagues Tomomi Sumida, who completed the Glycoside Hydrolase Family 123 page on March 17, and Wataru Saburi and Haruhide Mori, who completed the Glycoside Hydrolase Family 130 page on March 18. Members of these two GH families represent very distinct structures, specificities, and mechanisms, about which you can learn more on their individual pages. The high GH family numbers of these two groups reflect their comparatively recent addition to the CAZy Database and highlight the continuing evolution of the field through the discovery of new CAZymes.
23 February 2015: The sites that bind. Birte Svensson and Darrell Cockburn have completed the Surface Binding Site page within the CAZypedia Lexicon. Surface binding sites are substrate-binding regions found on the catalytic domain of carbohydrate-active enzymes and appear to play complementary roles to carbohydrate-binding modules in facilitating the action of polysaccharide-degrading glycoside hydrolases. Read more about these intriguing features and their distribution among CAZymes here.
20 February 2015: One for the Gals. Harry Gilbert has given the Carbohydrate Binding Module Family 62 page, which was authored by Cedric Montanier, Curator Approved status today. Functional and structural characterization of the archetypal CBM62 member from a Clostridium thermocellum xylanase revealed a strong affinity for galactose residues of either anomeric configuration on plant polysaccharides. Although the precise roles of this and other CBM62 members remains somewhat ambiguous, it is clear that these modules are relevant to the targeting of enzymes to the composite plant cell wall. Read more about the work of the all-star team that put CBM62 on the map (of CAZy families), here.
19 January 2015: Still in the high 70's today. Zui Fujimoto brought the Glycoside Hydrolase Family 78 page up to Curator Approved status today, making it CAZypedia's 97th approved GH page. GH78 is a family of archaeal, bacterial, and fungal alpha-L-rhamnosidases that cleave diverse flavonoid glycosides, polysaccharides, glycoproteins, and glycolipids from plants. Read more on these ecologically relevant enzymes here.
7 January 2015: Love your guts. CAZypedia is ringing in the new year with a new Glycoside Hydrolase Family 76 page by Spencer Williams. GH76 contains endo-acting α-mannanases, including members from the human gut bacterium Bacteroides thetaiotaomicron that enable us to degrade yeast mannans in our diet. A very recent publication in Nature, notably involving CAZypedia contributors Michael Suits, Al Boraston, Spencer Williams, Gideon Davies, Wade Abbott, and Harry Gilbert, has recently shed new light on the structure, mechanism, and biological function of these enzymes. Read more here!
11 September 2014: Another PL family done. Today, Richard McLean and Wade Abbott finished the Polysaccharide Lyase Family 22 page, bringing the number of Curator Approved PL pages in CAZypedia to a total of 5 (of 23). PL22 is a family of bacterial (and a handful of archeal) oligogalacturonide lyases (OGLs), archetypal members of which are highly specific for digalacturonate and Δ4,5-unsaturated digalacturonate i.e., they do not cleave polymeric α-(1,4)-linked galacturonan, a component of pectin. Wade performed a seminal crystallographic analysis of PL22, and he and Richard have produced a lucid distillation of the mechanism of catalysis in this family. Read more here!
9 September 2014: 2-for-1 Back to School Special. With the start of the new academic year, we are happy to report that two new Polysaccharide Lyase Family pages have recently been completed and given Curator Approved status. In August, Naotake Konno and Shinya Fushinobu produced the Polysaccharide Lyase Family 20 page, which describes this small (currently, 18 member) group of bacterial and fungal beta-(1-4)-glucuronan-cleaving enzymes. And, on the 7th of this month, Sine Larsen and Leila LoLeggio composed the Polysaccharide Lyase Family 4 page. Currently, PL4 is only known to contain rhamnogalacturonan lyases involved in pectin degradation, notably including many plant sequences in addition to bacterial and fungal members. We thank these Authors and Responsible Curators for their contributions and encourage our readers to check out these new pages.
2 July 2014: More on the alpha-amylase clan. We are pleased to report that Stefan Janecek has made another key contribution to CAZypedia by completing the Glycoside Hydrolase Family 77 page today. GH77 contains enzymes variously known as amylomaltases, 4-α-glucanotransferases, or disproportionating enzymes (D-enzymes in plants), which catalyze (1-4)-to-(1-4) transglycosylation of alpha-glucan chains and form part of the starch/glycogen debranching system. Together with GH13 and GH70, GH77 constitutes Clan GH-H, a clan of alpha-glucan-specific enzymes united by a common (β/α)8 catalytic domain fold. Stefan is the founder and main organiser of ALAMY - the international symposia on the alpha-amylase enzyme family - and has been a key person in producing the GH13, GH70, GH77 pages in CAZypedia; we are especially grateful for all his hard work and expertise!
23 June 2014: "LysM" domains in CAZypedia. The cohort of Carbohydrate Binding Module Families covered in CAZypedia continues to grow with the completion of the Carbohydrate Binding Module Family 50 by Takayuki Ohnuma and Toki Taira. CBM50 members are also known as LysM domains, which are found in a range of enzymes beyond glycoside hydrolases, including proteases, in which they are believed to facilitate targeting and degradation the bacterial cell wall. Read more here...!
14 May 2014: Two new CBM pages. We are pleased to report that Shinya Fushinobu has produced and given Curator Approved status to two new CBM pages. Carbohydrate Binding Module Family 28 contains Type B CBMs that target non-crystalline beta-glucan chains, while Carbohydrate Binding Module Family 42 members are Type C CBMs that bind terminal, non-reducing-end L-arabinofuranosyl residues, as found in xylans. Both families are likely to play key role in potentiating biomass degradation by their host organisms, and are therefore relevant to related biotechnological applications.
6 February 2014: Our second LPMO page. Glyn Hemsworth and Gideon Davies have just completed the Auxiliary Activity Family 11 page. AA11 is a very recently discovered family of copper-dependent, lytic polysaccharide mono-oxygenases (LPMO), whose defining member catalyzes the oxidative cleavage of chitin. The LPMO field is particularly exciting and rapidly evolving, and we are proud to present the AA11 page in CAZypedia so closely after the initial report on this family.
17 January 2014: More on CBMs. The Carbohydrate Binding Module Family 41 page was upgraded to Curator Approved status today by Alicia Lammerts van Bueren and Al Boraston. CBM41 is a family of alpha-glucan-binding modules, which are primarily associated with the pullulanases and debranching enzymes of Glycoside Hydrolase Family 13. Find out more here...!
6 January 2014: A new year, a new CBM page! The Carbohydrate Binding Module Family 6 page was completed and given Curator Approved status today by Author and Curator Mirjam Czjzek. CBM6 was originally defined based on the observation of xylan binding, however the diversity of substrate specificities in this family has now grown to include diverse beta-glucans, chitin, and even the marine polysaccharide agarose; remarkably, some CBM6 members also contain two distinct binding sites. The CBM6 page is CAZypedia's second Carbohydrate Binding Module Family page, and we look forward to the further expansion of this section in the new year!
18 December 2013: A new mannanase page. Today, Rohan Williams and Spencer Williams completed the Glycoside Hydrolase Family 113 page. GH113 is currently a very small family (120 members) with only one characterized member, the Alicyclobacillus acidocaldarius beta(1-4)-mannanase. The seminal crystal structure of this enzyme revealed GH113 to be a member of Clan GH-A. A recent publication from the Williams team and collaborators illuminated further details of the GH113 and GH26 transition states using designed inhibitor-enzyme complexes. Read more about this emerging family here!
6 October 2013: GH66 page upgraded to Curator Approved status. Today, Responsible Curator Zui Fujimoto formally approved the Glycoside Hydrolase Family 66 page, Authored by Ryuichiro Suzuki, as complete and ready for public viewing. GH66 is a very small family, currently containing ca. 60 members, of α(1-6)-glucan hydrolases (a.k.a. dextranases) and cyclo-isomalto-oligosaccharide glucanotransferases. Through a series of elegant studies including biochemical and crystallographic analyses, Dr. Fujimoto and his collaborators have provided direct insight into catalysis by this unique family. Read more about the long history of these enzymes here!
30 September 2013: Our first PL page! Wade Abbott finalized CAZypedia's first Polysaccharide Lyase Family page, PL2, today. As with our recent foray into CBM families (see our May 22 news item) the extension of CAZypedia to include the PLs ushers in a new phase in our development, and we are very much looking forward to the evolution of this new group of pages, spearheaded by Wade Abbott and Michael Suits. If you are an expert on any of the 22 PL families in the CAZy Database and would like to contribute to CAZypedia, please contact us.
19 September 2013: We are proud to announce the completion of CAZypedia's first Auxiliary Activity (AA) Family page! Paul Harris, one of the founding fathers of the family previously known as GH61, has composed a lucid summary of the history and state-of-the-art of Auxiliary Activity Family 9. The revelation that these enzymes are actually copper-dependent lytic polysaccharide mono-oxygenases (LPMO), and not classic cellulases as originally thought, is one of the most exciting discoveries in enzymatic biomass degradation in recent years. Read more about this fascinating class of enzymes on the here, and stay tuned for forthcoming page on the closely related AA10 family.
28 June 2013: CAZypedia was highlighted in a review article in Current Opinion in Structural Biology available online today. This review provides a succinct overview of some of the most exciting CAZyme structure-function studies in recent years, and we'd like to thank the authors, Shinya Fushinobu, Victor Alves, and Pedro Coutinho, for showcasing CAZypedia as well!
23 June 2013: Yet another Lexicon page. With the help of Motomitsu Kitaoka, Spencer Williams updated the Lexicon page on Phosphorylases today to Curator Approved status, bringing the number of completed Lexicon pages to 20. Phosphorylases catalyze glycosidic bond cleavage through nucleophilic substitution with phosphate (PO4--), and play important roles in, for example, storage polysaccharide breakdown by generating glucose-1-phosphate as a precursor to glycolysis. Notably, phosphorylases based on both glycoside hydrolase and glycosyltransferase protein folds are known. Read more about this important class of carbohydrate-active enzymes here.
22 May 2013: Our very first CBM page! Elizabeth Ficko-Blean and Alisdair Boraston finalized CAZypedia's first Carbohydrate Binding Module Family page, CBM32, today. This ushers in a new phase in CAZypedia's development, and we are looking forward to the continued evolution of this group of pages on these non-catalytic, substrate-binding, CAZyme-associated protein modules.
2 May 2013: Adding on to the Lexicon. Today Spencer Williams added the finishing touches to the Lexicon page on Transglycosylases. Transglycosylation - the ability to non-hydrolytically rearrange glycosidic bonds between one or more substrates - is a feature of many Glycoside hydrolases, especially those which use the retaining mechanism. In such enzymes, the covalent glycosyl-enzyme reaction intermediate can be intercepted by either water (yielding hydrolysis) or a sugar "acceptor" substrate (yielding transglycosylation). Although transglycosylation is generally a side activity of retaining enzymes, a handful are naturally very predominant Transglycosylases. See the Lexicon page to learn more, including specific examples!
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:
- Glycoside Hydrolase Family 74 (written by Katsuro Yaoi and Takuya Ishida, and curated by Katsuro Yaoi) is a family predominantly comprised of endo-glucanases that are specific for the plant polysaccharide xyloglucan (true xyloglucanases).
- Glycoside Hydrolase Family 95 (written and curated by Takane Katayama) is a family of 1,2-α-L-fucosidases, members of which cleave human milk oligosaccharides, blood group glycoconjugates, and/or xyloglucan oligosaccharides.
- Glycoside Hydrolase Family 117 (written by Etienne Rebuffet and curated by Mirjam Czjzek) is a small, newly created family of α-1,3-L-(3,6-anhydro)-galactosidases (neoagarobiose hydrolases), which catalyze the final step in the degradation of agars from red macroalgae in the marine environment.
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.
25 May 2010:
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.
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.