G J Davies

Summary

Affiliation: University of York
Country: UK

Publications

  1. ncbi request reprint Structural, thermodynamic, and kinetic analyses of tetrahydrooxazine-derived inhibitors bound to beta-glucosidases
    Tracey M Gloster
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom
    J Biol Chem 279:49236-42. 2004
  2. pmc Structure and kinetic investigation of Streptococcus pyogenes family GH38 alpha-mannosidase
    Michael D L Suits
    York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
    PLoS ONE 5:e9006. 2010
  3. doi request reprint Conformational analyses of the reaction coordinate of glycosidases
    Gideon J Davies
    Structural Biology Laboratory, Department of Chemistry, The University of York, United Kingdom
    Acc Chem Res 45:308-16. 2012
  4. ncbi request reprint Mapping the conformational itinerary of beta-glycosidases by X-ray crystallography
    G J Davies
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    Biochem Soc Trans 31:523-7. 2003
  5. ncbi request reprint Structural enzymology of carbohydrate-active enzymes: implications for the post-genomic era
    G J Davies
    Department of Chemistry, University of York, Heslington, York YO10 5DD, U K
    Biochem Soc Trans 30:291-7. 2002
  6. doi request reprint GlaxoSmithKline Award Lecture. The O-GlcNAc modification: three-dimensional structure, enzymology and the development of selective inhibitors to probe disease
    Gideon J Davies
    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
    Biochem Soc Trans 38:1179-88. 2010
  7. ncbi request reprint Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution
    Gideon J Davies
    Department of Chemistry, University of York, England
    Acta Crystallogr D Biol Crystallogr 61:190-3. 2005
  8. ncbi request reprint Recent structural insights into the expanding world of carbohydrate-active enzymes
    Gideon J Davies
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    Curr Opin Struct Biol 15:637-45. 2005
  9. ncbi request reprint Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase
    G J Davies
    Department of Chemistry, University of York, Heslington, U K
    Biochemistry 37:11707-13. 1998
  10. ncbi request reprint Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes
    A M Brzozowski
    Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, UK
    Biochemistry 39:9099-107. 2000

Collaborators

Detail Information

Publications101 found, 100 shown here

  1. ncbi request reprint Structural, thermodynamic, and kinetic analyses of tetrahydrooxazine-derived inhibitors bound to beta-glucosidases
    Tracey M Gloster
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom
    J Biol Chem 279:49236-42. 2004
    ....
  2. pmc Structure and kinetic investigation of Streptococcus pyogenes family GH38 alpha-mannosidase
    Michael D L Suits
    York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
    PLoS ONE 5:e9006. 2010
    ..Far less well understood is the observation that many bacterial species, predominantly but not exclusively pathogens and symbionts, also possess putative GH38 alpha-mannosidases whose activity and specificity is unknown...
  3. doi request reprint Conformational analyses of the reaction coordinate of glycosidases
    Gideon J Davies
    Structural Biology Laboratory, Department of Chemistry, The University of York, United Kingdom
    Acc Chem Res 45:308-16. 2012
    ..Conformational analyses highlight not only the itineraries used by enzymes, enabling their inhibition, but are also reflected in the nonenzymatic synthesis of glycosides, wherein chemists mimic strategies found in nature...
  4. ncbi request reprint Mapping the conformational itinerary of beta-glycosidases by X-ray crystallography
    G J Davies
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    Biochem Soc Trans 31:523-7. 2003
    ..Three-dimensional structures of enzyme complexes should now be able to drive the design of transition-state mimics that are specific for given enzymes, as opposed to being generic or merely fortuitous...
  5. ncbi request reprint Structural enzymology of carbohydrate-active enzymes: implications for the post-genomic era
    G J Davies
    Department of Chemistry, University of York, Heslington, York YO10 5DD, U K
    Biochem Soc Trans 30:291-7. 2002
    ....
  6. doi request reprint GlaxoSmithKline Award Lecture. The O-GlcNAc modification: three-dimensional structure, enzymology and the development of selective inhibitors to probe disease
    Gideon J Davies
    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
    Biochem Soc Trans 38:1179-88. 2010
    ..Such studies have questioned a causal link between O-GlcNAc and Type 2 diabetes, but do offer potential for the study, and perhaps the treatment, of tauopathies...
  7. ncbi request reprint Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution
    Gideon J Davies
    Department of Chemistry, University of York, England
    Acta Crystallogr D Biol Crystallogr 61:190-3. 2005
    ..Careful inspection of electron density suggests that the bound ligand could not have been formed through successive transglycosylations of acarbose and must also have featured maltose or maltooligosaccharides as an acceptor...
  8. ncbi request reprint Recent structural insights into the expanding world of carbohydrate-active enzymes
    Gideon J Davies
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    Curr Opin Struct Biol 15:637-45. 2005
    ....
  9. ncbi request reprint Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase
    G J Davies
    Department of Chemistry, University of York, Heslington, U K
    Biochemistry 37:11707-13. 1998
    ..Finally, hydrolysis of this intermediate yields a product complex in which the sugar is bound in a partially disordered mode, consistent with unfavorable interactions and low product affinity...
  10. ncbi request reprint Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes
    A M Brzozowski
    Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, UK
    Biochemistry 39:9099-107. 2000
    ....
  11. ncbi request reprint Structure of the Bacillus agaradherans family 5 endoglucanase at 1.6 A and its cellobiose complex at 2.0 A resolution
    G J Davies
    Department of Chemistry, University of York, Heslington, England
    Biochemistry 37:1926-32. 1998
    ....
  12. ncbi request reprint Substrate specificity in glycoside hydrolase family 10. Structural and kinetic analysis of the Streptomyces lividans xylanase 10A
    V Ducros
    Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
    J Biol Chem 275:23020-6. 2000
    ....
  13. ncbi request reprint Three-dimensional structures of the Mn and Mg dTDP complexes of the family GT-2 glycosyltransferase SpsA: a comparison with related NDP-sugar glycosyltransferases
    N Tarbouriech
    Department of Chemistry, Structural Biology Laboratory, Heslington, Y010 5DD, UK
    J Mol Biol 314:655-61. 2001
    ..Family GT-2 enzymes, together with enzymes from families 7, 13 and 43, appear to form a clan of related structures with identical catalytic apparatus and reaction mechanism...
  14. ncbi request reprint Atomic resolution structure of endoglucanase Cel5A in complex with methyl 4,4II,4III,4IV-tetrathio-alpha-cellopentoside highlights the alternative binding modes targeted by substrate mimics
    A Varrot
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York Y010 5DD, England
    Acta Crystallogr D Biol Crystallogr 57:1739-42. 2001
    ..These two binding modes may reflect different steps in the binding and catalytic process...
  15. ncbi request reprint Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms
    S J Charnock
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, UK
    Biochemistry 38:6380-5. 1999
    ..0 and 1.7 A, respectively. These complexes, together with the sequence conservation, begin to shed light on the mechanism of this ubiquitous family of inverting glycosyltransferases...
  16. ncbi request reprint Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre
    E Sabini
    Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, England
    Acta Crystallogr D Biol Crystallogr 57:1344-7. 2001
    ..The structure of the covalent 2-deoxy-2-fluoroxylobiosyl-enzyme intermediate has been extended to atomic (1.1 A) resolution...
  17. ncbi request reprint Oligosaccharide specificity of a family 7 endoglucanase: insertion of potential sugar-binding subsites
    G J Davies
    Department of Chemistry, University of York, Heslington, UK
    J Biotechnol 57:91-100. 1997
    ..On phosphoric acid swollen cellulose there is a small (30%), but significant, decrease in the apparent KM indicating that the double mutant may indeed exhibit stronger binding to longer polymeric substrates...
  18. ncbi request reprint Structure of the laccase from Coprinus cinereus at 1.68 A resolution: evidence for different 'type 2 Cu-depleted' isoforms
    V Ducros
    Department of Chemistry, University of York, Heslington, York YO10 5DD, England
    Acta Crystallogr D Biol Crystallogr 57:333-6. 2001
    ..The three-dimensional structure of the 'blue' multi-copper oxidase laccase from the fungus Coprinus cinereus at 1.68 A reveals the structural basis for isoforms of the type 2 Cu-depleted species...
  19. ncbi request reprint The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: structure and biochemistry of the Clostridium thermocellum X6b domain
    S J Charnock
    Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, U K
    Biochemistry 39:5013-21. 2000
    ..In view of the structural and carbohydrate-binding properties of X6b, it is proposed that this and related modules be re-assigned as family 22 carbohydrate-binding modules...
  20. ncbi request reprint Characterization of a novel pectate lyase, Pel10A, from Pseudomonas cellulosa
    S J Charnock
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
    Acta Crystallogr D Biol Crystallogr 57:1141-3. 2001
    ..They belong to space group P2(1), with unit-cell parameters a = 47.7, b = 106.1, c = 55.4 A, beta = 92.0 degrees, and have two molecules in the asymmetric unit. The crystals diffract beyond 1.5 A using synchrotron radiation...
  21. ncbi request reprint Cloning, crystallization and preliminary X-ray analysis of a nucleotide-diphospho-sugar transferase spsA from Bacillus subtilis
    S J Charnock
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
    Acta Crystallogr D Biol Crystallogr 55:677-8. 1999
    ..They belong to space group C2221, with unit-cell dimensions a = 42.4, b = 142.0, c = 81.4 A and with one molecule of spsA in the asymmetric unit. The crystals diffract beyond 1.5 A using synchrotron radiation...
  22. ncbi request reprint The Streptomyces lividans family 12 endoglucanase: construction of the catalytic cre, expression, and X-ray structure at 1.75 A resolution
    G Sulzenbacher
    Department of Chemistry, University of York, Heslington, York YO1 5DD, England, UK
    Biochemistry 36:16032-9. 1997
    ..0 A and are located approximately 15 A from one end of the cleft, implying a -3 to +2 active site...
  23. ncbi request reprint The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution
    G Sulzenbacher
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, Y010 5DD, U K
    Biochemistry 38:4826-33. 1999
    ....
  24. pmc Structure and function of Humicola insolens family 6 cellulases: structure of the endoglucanase, Cel6B, at 1.6 A resolution
    G J Davies
    Department of Chemistry, University of York, Heslington, York YO10 5DD, U K
    Biochem J 348:201-7. 2000
    ....
  25. ncbi request reprint How family 26 glycoside hydrolases orchestrate catalysis on different polysaccharides: structure and activity of a Clostridium thermocellum lichenase, CtLic26A
    Edward J Taylor
    York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom
    J Biol Chem 280:32761-7. 2005
    ..We suggest a different conformational itinerary for the GH26 enzymes active on gluco-configured substrates...
  26. pmc Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases
    Simon J Charnock
    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
    Proc Natl Acad Sci U S A 99:12067-72. 2002
    ....
  27. ncbi request reprint Crystallization and preliminary X-ray analysis of the 6-phospho-alpha-glucosidase from Bacillus subtilis
    A Varrot
    Department of Chemistry, University of York, Heslington, York YO10 5DD, England
    Acta Crystallogr D Biol Crystallogr 55:1212-4. 1999
    ..They diffract beyond 2.2 A using synchrotron radiation and belong to the space group I222 (or its enantiomorph) with unit-cell dimensions a = 83.26, b = 102.56, c = 145.31 A and contain a single molecule of GlvA in the asymmetric unit...
  28. pmc Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose
    Simon J Charnock
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
    Proc Natl Acad Sci U S A 99:14077-82. 2002
    ....
  29. doi request reprint Probing the beta-1,3:1,4 glucanase, CtLic26A, with a thio-oligosaccharide and enzyme variants
    Victoria A Money
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, U K YO10 5YW
    Org Biomol Chem 6:851-3. 2008
    ..The substrate binding regions of a beta-1,3:1,4 glucanase are revealed through structural analysis with a thio-oligosaccharide and kinetics of enzyme variants...
  30. pmc Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora
    Tracey M Gloster
    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK
    Chem Biol 15:1058-67. 2008
    ..1H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining alpha-galactosidase...
  31. ncbi request reprint Direct observation of the protonation state of an imino sugar glycosidase inhibitor upon binding
    Annabelle Varrot
    Department of Chemistry, Structural Biology Laboratory, The University of York, Heslington, York YO10 5YW, United Kingdom
    J Am Chem Soc 125:7496-7. 2003
    ..Surprisingly, both the enzymatic nucleophile and the acid/base are unprotonated in the complex...
  32. ncbi request reprint Dissection of conformationally restricted inhibitors binding to a beta-glucosidase
    Tracey M Gloster
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK
    Chembiochem 7:738-42. 2006
  33. ncbi request reprint Glycosidase inhibition: an assessment of the binding of 18 putative transition-state mimics
    Tracey M Gloster
    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
    J Am Chem Soc 129:2345-54. 2007
    ....
  34. pmc Glycosidase inhibition: assessing mimicry of the transition state
    Tracey M Gloster
    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    Org Biomol Chem 8:305-20. 2010
    ..A number of criteria have been proposed to ascertain which of these inhibitors are true transition state mimics, but these features have only be critically investigated in a very few cases...
  35. ncbi request reprint Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity
    Rebecca J Dennis
    York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5YW, UK
    Nat Struct Mol Biol 13:365-71. 2006
    ..Mutagenesis and kinetics studies show that the bacterial enzyme, very similarly to its human counterpart, operates via an unusual 'substrate-assisted' catalytic mechanism, which will inform the rational design of enzyme inhibitors...
  36. pmc Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus
    Carlos Martinez-Fleites
    Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5YW, UK
    Biochem J 390:19-27. 2005
    ..Despite the strong conservation of the sucrose-recognition site observed in LsdA, Bs levansucrase and GH32 family Thermotoga maritima invertase, structural differences appear around residues involved in the transfructosylation reaction...
  37. ncbi request reprint Validation tools: can they indicate the information content of macromolecular crystal structures?
    E J Dodson
    University of York, York, YO1 5DD, UK
    Structure 6:685-90. 1998
    ..Validation tools will evolve as more appropriate statistical techniques and new information, such as that from proteins analysed at atomic resolution, becomes available...
  38. ncbi request reprint The use of forced protein evolution to investigate and improve stability of family 10 xylanases. The production of Ca2+-independent stable xylanases
    Simon R Andrews
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    J Biol Chem 279:54369-79. 2004
    ..This study demonstrates how forced protein evolution can be used to introduce enhanced stability into industrially relevant enzymes while removing calcium as a major stability determinant...
  39. ncbi request reprint NAD+ and metal-ion dependent hydrolysis by family 4 glycosidases: structural insight into specificity for phospho-beta-D-glucosides
    Annabelle Varrot
    York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, UK
    J Mol Biol 346:423-35. 2005
    ....
  40. ncbi request reprint Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold
    Didier Nurizzo
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
    Nat Struct Biol 9:665-8. 2002
    ..Three carboxylates deep in the active site groove provide the general acid and base components for glycosidic bond hydrolysis with inversion of anomeric configuration...
  41. ncbi request reprint Structure and activity of two metal ion-dependent acetylxylan esterases involved in plant cell wall degradation reveals a close similarity to peptidoglycan deacetylases
    Edward J Taylor
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
    J Biol Chem 281:10968-75. 2006
    ..E., Schuettelkopf, A. W., MacRae, J. I., and Aalten, D. M. (2005) Proc. Natl. Acad. Sci. U. S. A., 102, 15429-15434), which form the NodB deacetylase "superfamily."..
  42. ncbi request reprint The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A
    Didier Nurizzo
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, United Kingdom
    Structure 10:547-56. 2002
    ....
  43. ncbi request reprint Structural studies of the beta-glycosidase from Sulfolobus solfataricus in complex with covalently and noncovalently bound inhibitors
    Tracey M Gloster
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom
    Biochemistry 43:6101-9. 2004
    ..The inhibition of the beta-glycosidase from S. solfataricus by hydroximolactams is discussed in light of the emerging work on family GH1 glycosidase inhibition by a spectrum of putative transition-state mimics...
  44. ncbi request reprint Structural, kinetic, and thermodynamic analysis of glucoimidazole-derived glycosidase inhibitors
    Tracey M Gloster
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom
    Biochemistry 45:11879-84. 2006
    ....
  45. ncbi request reprint Iminosugar glycosidase inhibitors: structural and thermodynamic dissection of the binding of isofagomine and 1-deoxynojirimycin to beta-glucosidases
    David L Zechel
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
    J Am Chem Soc 125:14313-23. 2003
    ..1 A resolution, reveal that additional ordering of bound solvent may present an entropic penalty to 1-deoxynojirimycin binding that does not penalize isofagomine...
  46. ncbi request reprint Insights into trehalose synthesis provided by the structure of the retaining glucosyltransferase OtsA
    Robert P Gibson
    Department of Chemistry, The University of York, York YO10 5YW, Heslington, United Kingdom
    Chem Biol 9:1337-46. 2002
    ..The overall structure and the intimate details of the catalytic machinery reveal a striking similarity to glycogen phosphorylase, indicating a strong evolutionary link and suggesting a common catalytic mechanism...
  47. doi request reprint Analysis of the reaction coordinate of alpha-L-fucosidases: a combined structural and quantum mechanical approach
    Alicia Lammerts van Bueren
    York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5YW, UK
    J Am Chem Soc 132:1804-6. 2010
    ..Analysis of an imino sugar inhibitor is consistent with tight binding of a chair-conformed charged species...
  48. ncbi request reprint Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate binding module, TmCBM27
    Alisdair B Boraston
    Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
    Structure 11:665-75. 2003
    ....
  49. ncbi request reprint DNA-nogalamycin interactions: the crystal structure of d(TGATCA) complexed with nogalamycin
    C K Smith
    Department of Chemistry, University of York, Heslington, England
    Biochemistry 34:415-25. 1995
    ..The position of the drug in this complex is stabilized by a number of nonbonded forces including van der Waals interactions and extensive direct and solvent-mediated hydrogen bonds to the DNA duplex...
  50. ncbi request reprint Direct experimental observation of the hydrogen-bonding network of a glycosidase along its reaction coordinate revealed by atomic resolution analyses of endoglucanase Cel5A
    Annabelle Varrot
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, England
    Acta Crystallogr D Biol Crystallogr 59:447-52. 2003
    ....
  51. ncbi request reprint Structure and kinetics of a monomeric glucosamine 6-phosphate deaminase: missing link of the NagB superfamily?
    Florence Vincent
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, UK
    J Biol Chem 280:19649-55. 2005
    ..The structure completes the NagB superfamily structural landscape and thus allows further interrogation of genomic data in terms of the regulation of NagB and the metabolic fate(s) of glucosamine 6-phosphate...
  52. doi request reprint Structural analyses of enzymes involved in the O-GlcNAc modification
    Carlos Martinez-Fleites
    York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5YW, UK
    Biochim Biophys Acta 1800:122-33. 2010
    ..These have informed the design and/or subsequent analysis of inhibitors of this enzyme which have found great use in the chemical dissection of the O-GlcNAc in vivo, as described by Macauley and Vocadlo elsewhere in this issue...
  53. ncbi request reprint Crystal structures of Clostridium thermocellum xyloglucanase, XGH74A, reveal the structural basis for xyloglucan recognition and degradation
    Carlos Martinez-Fleites
    York Structural Biology Laboratory, Department of Chemitry, University of York, York YO10 5YW, United Kingdom
    J Biol Chem 281:24922-33. 2006
    ....
  54. ncbi request reprint Multifunctional xylooligosaccharide/cephalosporin C deacetylase revealed by the hexameric structure of the Bacillus subtilis enzyme at 1.9A resolution
    Florence Vincent
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    J Mol Biol 330:593-606. 2003
    ..1.1.72) and cephalosporin C deacetylase (EC 3.1.1.41) enzymes of the CE-7 family represent a single class of proteins with a multifunctional deacetylase activity against a range of small substrates...
  55. ncbi request reprint Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules
    Sheelan Jamal-Talabani
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom
    Structure 12:1177-87. 2004
    ..CBM36 is one of an emerging spectrum of carbohydrate binding modules that increasingly find applications in industry and display great potential for mapping the "glyco-architecture" of plant cells...
  56. pmc Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum
    Edward J Taylor
    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
    Biochem J 395:31-7. 2006
    ....
  57. ncbi request reprint Insights into the synthesis of lipopolysaccharide and antibiotics through the structures of two retaining glycosyltransferases from family GT4
    Carlos Martinez-Fleites
    York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom
    Chem Biol 13:1143-52. 2006
    ..Structural information is discussed with respect to the evolution of GTs and the therapeutic significance of the two enzymes...
  58. ncbi request reprint Characterization and three-dimensional structures of two distinct bacterial xyloglucanases from families GH5 and GH12
    Tracey M Gloster
    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
    J Biol Chem 282:19177-89. 2007
    ..The differential strategies for the accommodation of the side chains of xyloglucan presumably facilitate the action of these microbial hydrolases in milieus where diverse and differently substituted substrates may be encountered...
  59. ncbi request reprint Crystal structure of an N-terminal fragment of the DNA gyrase B protein
    D B Wigley
    Department of Chemistry, York University, Heslington, UK
    Nature 351:624-9. 1991
    ..The C-terminal domains form the sides of a 20 A hole through the protein dimer which may play a role in DNA strand passage during the supercoiling reaction...
  60. pmc Structure of a flavonoid glucosyltransferase reveals the basis for plant natural product modification
    Wendy Offen
    Department of Chemistry, University of York, York, UK
    EMBO J 25:1396-405. 2006
    ..These structures, in tandem with kinetic dissection of activity, provide the foundation for understanding the mechanism of these enzymes in small molecule homeostasis...
  61. doi request reprint Structural insight into the mechanism of streptozotocin inhibition of O-GlcNAcase
    Yuan He
    Department of Chemistry, Structural Biology Laboratory, The University of York, Heslington, York, YO10 5YW, UK
    Carbohydr Res 344:627-31. 2009
    ..The active site of the BtGH84 is considerably deformed upon STZ binding and as a result the catalytic machinery is expelled from the binding cavity...
  62. ncbi request reprint A glycosynthase catalyst for the synthesis of flavonoid glycosides
    Min Yang
    Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
    Angew Chem Int Ed Engl 46:3885-8. 2007
  63. ncbi request reprint Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases
    Victoria A Money
    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
    Angew Chem Int Ed Engl 45:5136-40. 2006
  64. doi request reprint Structure of an O-GlcNAc transferase homolog provides insight into intracellular glycosylation
    Carlos Martinez-Fleites
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, UK
    Nat Struct Mol Biol 15:764-5. 2008
    ..UDP-GlcNAc:polypeptidyl transferase (OGT) catalyzes O-GlcNAc addition. The structure of an intact OGT homolog and kinetic analysis of human OGT variants reveal a contiguous superhelical groove that directs substrates to the active site...
  65. ncbi request reprint Molecular basis for trehalase inhibition revealed by the structure of trehalase in complex with potent inhibitors
    Robert P Gibson
    Department of Chemistry, York Structural Biology Laboratory, York, YO, UK
    Angew Chem Int Ed Engl 46:4115-9. 2007
  66. ncbi request reprint Structural basis for cyclophellitol inhibition of a beta-glucosidase
    Tracey M Gloster
    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK YO10 5YW
    Org Biomol Chem 5:444-6. 2007
    ..The structural basis for beta-glucosidase inhibition by cyclophellitol is demonstrated using X-ray crystallography, enzyme kinetics and mass spectrometry...
  67. ncbi request reprint Anatomy of glycosynthesis: structure and kinetics of the Humicola insolens Cel7B E197A and E197S glycosynthase mutants
    Valerie M A Ducros
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom
    Chem Biol 10:619-28. 2003
    ..Kinetic analysis shows that the E197S mutant is considerably more active than the corresponding alanine mutant due to a 40-fold increase in k(cat)...
  68. ncbi request reprint X-ray crystal structure of a non-crystalline cellulose-specific carbohydrate-binding module: CBM28
    Sheelan Jamal
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, UK
    J Mol Biol 339:253-8. 2004
    ..The ligand-binding site "topographies" of CBMs from families 28, 17 and 4 begins to shed light on the differential recognition of non-crystalline cellulose by multi-modular plant cell wall-degrading enzymes...
  69. ncbi request reprint The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily
    Florence Vincent
    Department of Chemistry, The University of York, Heslington, York, YO10 5YW, United Kingdom
    J Biol Chem 279:2809-16. 2004
    ..We believe that this is the first sugar deacetylase to utilize this fold and catalytic mechanism...
  70. ncbi request reprint Common inhibition of both beta-glucosidases and beta-mannosidases by isofagomine lactam reflects different conformational itineraries for pyranoside hydrolysis
    Florence Vincent
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5YW, UK
    Chembiochem 5:1596-9. 2004
  71. ncbi request reprint Structural basis for ligand binding and processivity in cellobiohydrolase Cel6A from Humicola insolens
    Annabelle Varrot
    Department of Chemistry, University of York, Heslington, Y010 5YW, York, United Kingdom
    Structure 11:855-64. 2003
    ..Movement of ligand is facilitated by extensive solvent-mediated interactions and through flexibility in the hydrophobic surfaces provided by a sheath of tryptophan residues...
  72. ncbi request reprint Mycobacterium tuberculosis strains possess functional cellulases
    Annabelle Varrot
    York Structural Biology Laboratory, Department of Chemistry, University of York, York, Y010 5YW, United Kingdom
    J Biol Chem 280:20181-4. 2005
    ....
  73. ncbi request reprint Characterization of Escherichia coli OtsA, a trehalose-6-phosphate synthase from glycosyltransferase family 20
    Robert P Gibson
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
    Acta Crystallogr D Biol Crystallogr 58:349-51. 2002
    ..The second form has unit-cell parameters a = b = 141.9, c = 317.8 A and displays the apparent space group P4(2). These crystals diffract beyond 2 A resolution, but display merohedral twinning...
  74. ncbi request reprint The donor subsite of trehalose-6-phosphate synthase: binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 A resolution
    Robert P Gibson
    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
    J Biol Chem 279:1950-5. 2004
    ..Both the relative orientation of the two domains and substantial (up to 10 A) movements of an N-terminal loop (residues 9-22) characterize the more open "relaxed" conformation of the binary UDP-sugar complexes reported here...
  75. ncbi request reprint Structure of the Humicola insolens cellobiohydrolase Cel6A D416A mutant in complex with a non-hydrolysable substrate analogue, methyl cellobiosyl-4-thio-beta-cellobioside, at 1.9 A
    Annabelle Varrot
    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York Y010 5YW, England
    Acta Crystallogr D Biol Crystallogr 58:2201-4. 2002
    ..1999), Structure, 7, 1035-1045], but the active-centre N-terminal loop of the H. insolens enzyme is found in a more open conformation than described for previous structures...
  76. doi request reprint The crystal structure of a family GH25 lysozyme from Bacillus anthracis implies a neighboring-group catalytic mechanism with retention of anomeric configuration
    Carlos Martinez-Fleites
    Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5YW, United Kingdom
    Carbohydr Res 344:1753-7. 2009
    ....
  77. ncbi request reprint Structure of a carbohydrate esterase from Bacillus anthracis
    Leoni Oberbarnscheidt
    York Structural Biology Laboratory, University of York, York YO10 5YW, United Kingdom
    Proteins 66:250-2. 2007
  78. doi request reprint The X-ray crystal structure of an Arthrobacter protophormiae endo-beta-N-acetylglucosaminidase reveals a (beta/alpha)(8) catalytic domain, two ancillary domains and active site residues key for transglycosylation activity
    Zhenlian Ling
    Department of Biology, University of York, UK
    J Mol Biol 389:1-9. 2009
    ....
  79. doi request reprint Visualizing the reaction coordinate of an O-GlcNAc hydrolase
    Yuan He
    York Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5YW, UK
    J Am Chem Soc 132:1807-9. 2010
    ..Here we define the reaction coordinate using chemical approaches and directly observe both a Michaelis complex and the oxazoline intermediate...
  80. doi request reprint Structural and biochemical evidence for a boat-like transition state in beta-mannosidases
    Louise E Tailford
    Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
    Nat Chem Biol 4:306-12. 2008
    ....
  81. ncbi request reprint An evolving hierarchical family classification for glycosyltransferases
    Pedro M Coutinho
    Architecture et Fonction des Macromolecules Biologiques, UMR6098, CNRS and Universités d Aix Marseille I and II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    J Mol Biol 328:307-17. 2003
    ....
  82. ncbi request reprint The alpha-glucuronidase, GlcA67A, of Cellvibrio japonicus utilizes the carboxylate and methyl groups of aldobiouronic acid as important substrate recognition determinants
    Tibor Nagy
    School of Cell and Molecular Biosciences, The University of Newcastle upon Tyne, United Kingdom
    J Biol Chem 278:20286-92. 2003
    ..Replacing the two tryptophan residues that stack against the sugar rings of the substrate with alanine (W160A and W543A) greatly reduced activity...
  83. pmc The crystal structure of two macrolide glycosyltransferases provides a blueprint for host cell antibiotic immunity
    David N Bolam
    Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
    Proc Natl Acad Sci U S A 104:5336-41. 2007
    ..The data reported here provide structural insight into the mechanism of resistance to both endogenous and exogenous antibiotics, and will provide a platform for the future redesign of these catalysts for antibiotic remodelling...
  84. ncbi request reprint Glycosidase mechanisms
    Andrea Vasella
    Laboratorium fur Organische Chemie, ETH Honggerberg, HCI H317, CH 8093 Zurich, Switzerland
    Curr Opin Chem Biol 6:619-29. 2002
    ..3D-structure in synergy with transition-state mimicry opens the way for mechanistic interpretation of enzyme inhibition and for the development of therapeutic agents...
  85. ncbi request reprint Probing the mechanism of ligand recognition in family 29 carbohydrate-binding modules
    James Flint
    Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
    J Biol Chem 280:23718-26. 2005
    ..The interactions of CBM29-2 with the O2 of glucose or mannose contribute little to binding affinity, explaining why this CBM displays dual gluco/manno specificity...
  86. ncbi request reprint Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains
    Joanna Henshaw
    Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
    J Biol Chem 281:17099-107. 2006
    ....
  87. pmc Functional analysis of a group A streptococcal glycoside hydrolase Spy1600 from family 84 reveals it is a beta-N-acetylglucosaminidase and not a hyaluronidase
    William L Sheldon
    Biomolecular and Biomedical Research Centre, School of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
    Biochem J 399:241-7. 2006
    ..Since these enzymes do not have detectable hyaluronidase activity, many family 84 glycoside hydrolases are most likely incorrectly annotated as hyaluronidases...
  88. ncbi request reprint Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+ -dependent phospho-alpha-glucosidase from Bacillus subtilis
    Shyamala S Rajan
    Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    Structure 12:1619-29. 2004
    ....
  89. ncbi request reprint Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A
    Fernando M V Dias
    CIISA Faculdade de Medicina Veterinaria, Universidade Tecnica de Lisboa, Rua Prof Cid dos Santos, 1300 477 Lisboa, Portugal
    J Biol Chem 279:25517-26. 2004
    ..This insertion forms a "double" steric barrier, formed by two short beta-strands that function to "block" the substrate binding cleft at the edge of the -1 subsite forming the "exo" active center topology of CmMan5A...
  90. ncbi request reprint Ligand-mediated dimerization of a carbohydrate-binding molecule reveals a novel mechanism for protein-carbohydrate recognition
    James Flint
    School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Agriculture Building, Newcastle upon Tyne NE1 7RU, UK
    J Mol Biol 337:417-26. 2004
    ....
  91. ncbi request reprint Crystallization and preliminary X-ray diffraction analysis of levansucrase (LsdA) from Gluconacetobacter diazotrophicus SRT4
    Carlos Martinez-Fleites
    Physical Chemistry Division, Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana 10600, Cuba
    Acta Crystallogr D Biol Crystallogr 60:181-3. 2004
    ..5 A under cryogenic conditions using synchrotron radiation. LsdA crystals belong to the orthorhombic space group P22(1)2(1) or P2(1)2(1)2, with unit-cell parameters a = 53.80, b = 119.39, c = 215.10 A...
  92. ncbi request reprint Mannose foraging by Bacteroides thetaiotaomicron: structure and specificity of the beta-mannosidase, BtMan2A
    Louise E Tailford
    Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
    J Biol Chem 282:11291-9. 2007
    ..The catalytic properties of BtMan2A are consistent with the flexible nutrient acquisition displayed by the colonic bacterium...
  93. ncbi request reprint Structural dissection and high-throughput screening of mannosylglycerate synthase
    James Flint
    Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Medical School, Newcastle upon Tyne NE2 4HH, UK
    Nat Struct Mol Biol 12:608-14. 2005
    ..Nucleotide specificity is as important in GDP-D-mannose recognition as the nature of the donor sugar...
  94. ncbi request reprint Differential oligosaccharide recognition by evolutionarily-related beta-1,4 and beta-1,3 glucan-binding modules
    Alisdair B Boraston
    Protein Engineering Network of Centres of Excellence, Edmonton, Alberta, Canada T6G 2S2
    J Mol Biol 319:1143-56. 2002
    ..Thermodynamics interpreted in the light of structural information highlights the differential role of water in the interaction of these CBMs with their respective oligosaccharide ligands...
  95. pmc Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex
    Ana L Carvalho
    Rede de Química e Tecnologia Centro de Química Fina e Biotecnologia REQUIMTE CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829 516 Caparica, Portugal
    Proc Natl Acad Sci U S A 100:13809-14. 2003
    ..The structure provides an explanation for the lack of cross-species recognition between cohesin-dockerin pairs and thus provides a blueprint for the rational design, construction, and exploitation of these catalytic assemblies...
  96. ncbi request reprint The mechanisms by which family 10 glycoside hydrolases bind decorated substrates
    Gavin Pell
    School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Agriculture Building, Newcastle upon Tyne NE1 7RU, United Kingdom
    J Biol Chem 279:9597-605. 2004
    ..The data described in this report and in the accompanying paper indicate that the complementarity in the binding of decorated substrates between the glycone and aglycone regions appears to be a conserved feature of GH10 xylanases...
  97. pmc Evidence for a dual binding mode of dockerin modules to cohesins
    Ana Luisa Carvalho
    Rede de Química e Tecnologia Centro de Química Fina e Biotecnologia REQUIMTE CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829 516 Caparica, Portugal
    Proc Natl Acad Sci U S A 104:3089-94. 2007
    ....
  98. ncbi request reprint Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases
    Gavin Pell
    School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Agriculture Bldg, Newcastle upon Tyne NE1 7RU
    J Biol Chem 279:11777-88. 2004
    ..The generic importance of using CjXyn10C as a template in predicting the biochemical properties of GH10 xylanases is discussed...
  99. pmc Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A
    Mark R Proctor
    Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kindgom
    Proc Natl Acad Sci U S A 102:2697-702. 2005
    ..The introduction of subtle changes informed by comparative 3D structural and genomic data can lead to fundamental changes in the mode of action of these enzymes...
  100. ncbi request reprint Insights into the structural determinants of cohesin-dockerin specificity revealed by the crystal structure of the type II cohesin from Clostridium thermocellum SdbA
    Ana L Carvalho
    REQUIMTE CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829 516 Caparica, Portugal
    J Mol Biol 349:909-15. 2005
    ....
  101. ncbi request reprint The Clostridium cellulolyticum dockerin displays a dual binding mode for its cohesin partner
    Benedita A Pinheiro
    Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinaria, Universidade Tecnica de Lisboa, Lisboa, Portugal
    J Biol Chem 283:18422-30. 2008
    ..The biological significance of the plasticity in dockerin-cohesin recognition, observed here in C. cellulolyticum and reported previously in C. thermocellum, is discussed...