D W Rice

Summary

Affiliation: University of Sheffield
Country: UK

Publications

  1. ncbi request reprint Insights into the mechanisms of homologous recombination from the structure of RuvA
    D W Rice
    Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
    Curr Opin Struct Biol 7:798-803. 1997
  2. ncbi request reprint A mechanism of drug action revealed by structural studies of enoyl reductase
    C Baldock
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
    Science 274:2107-10. 1996
  3. ncbi request reprint Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction
    J B Rafferty
    Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Science 274:415-21. 1996
  4. ncbi request reprint Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution
    D Hargreaves
    Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, UK
    Nat Struct Biol 5:441-6. 1998
  5. ncbi request reprint Common themes in redox chemistry emerge from the X-ray structure of oilseed rape (Brassica napus) enoyl acyl carrier protein reductase
    J B Rafferty
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
    Structure 3:927-38. 1995
  6. ncbi request reprint Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase
    S N Ruzheinikov
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
    Structure 9:789-802. 2001
  7. ncbi request reprint The structure and domain organization of Escherichia coli isocitrate lyase
    K L Britton
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:1209-18. 2001
  8. ncbi request reprint A study of the structure-activity relationship for diazaborine inhibition of Escherichia coli enoyl-ACP reductase
    C W Levy
    Krebs Institute for Research, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
    J Mol Biol 309:171-80. 2001
  9. ncbi request reprint The 1.2 A structure of a novel quorum-sensing protein, Bacillus subtilis LuxS
    S N Ruzheinikov
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
    J Mol Biol 313:111-22. 2001
  10. ncbi request reprint Crystallization and quaternary structure analysis of an Lrp-like regulatory protein from the hyperthermophile Pyrococcus furiosus
    S E Sedelnikova
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:886-8. 2001

Collaborators

Detail Information

Publications40

  1. ncbi request reprint Insights into the mechanisms of homologous recombination from the structure of RuvA
    D W Rice
    Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
    Curr Opin Struct Biol 7:798-803. 1997
    ..This suggests that the four arms of the junction are held by RuvA in a fourfold symmetric arrangement and has fuelled ideas on the way in which components of the Ruv complex combine to catalyse the process of homologous recombination...
  2. ncbi request reprint A mechanism of drug action revealed by structural studies of enoyl reductase
    C Baldock
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
    Science 274:2107-10. 1996
    ....
  3. ncbi request reprint Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction
    J B Rafferty
    Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    Science 274:415-21. 1996
    ..The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC...
  4. ncbi request reprint Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution
    D Hargreaves
    Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, UK
    Nat Struct Biol 5:441-6. 1998
    ..The open structure of the junction stabilized by RuvA binding exposes a DNA surface that could be bound by the RuvC endonuclease to promote resolution...
  5. ncbi request reprint Common themes in redox chemistry emerge from the X-ray structure of oilseed rape (Brassica napus) enoyl acyl carrier protein reductase
    J B Rafferty
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
    Structure 3:927-38. 1995
    ..Highly elevated levels of the NADH-dependent enzyme are found during lipid deposition in maturing seeds of oilseed rape (Brassica napus)...
  6. ncbi request reprint Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase
    S N Ruzheinikov
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
    Structure 9:789-802. 2001
    ..Finally, the structure suggests that the NAD(+) binding domain of GlyDH may be related to that of the classical Rossmann fold by switching the sequence order of the two mononucleotide binding folds that make up this domain...
  7. ncbi request reprint The structure and domain organization of Escherichia coli isocitrate lyase
    K L Britton
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:1209-18. 2001
    ....
  8. ncbi request reprint A study of the structure-activity relationship for diazaborine inhibition of Escherichia coli enoyl-ACP reductase
    C W Levy
    Krebs Institute for Research, Department of Molecular Biology and Biotechnology, University of Sheffield, UK
    J Mol Biol 309:171-80. 2001
    ..Additionally, diazaborine binding provides insights into the pocket on the enzyme surface occupied by the growing fatty acid chain...
  9. ncbi request reprint The 1.2 A structure of a novel quorum-sensing protein, Bacillus subtilis LuxS
    S N Ruzheinikov
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
    J Mol Biol 313:111-22. 2001
    ..The autoinducer-2 signalling pathway has been linked to aspects of bacterial virulence and pathogenicity. The structural data on LuxS will provide opportunities for targeting this enzyme for the rational design of new antibiotics...
  10. ncbi request reprint Crystallization and quaternary structure analysis of an Lrp-like regulatory protein from the hyperthermophile Pyrococcus furiosus
    S E Sedelnikova
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:886-8. 2001
    ....
  11. ncbi request reprint Crystallographic analysis of triclosan bound to enoyl reductase
    A Roujeinikova
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, UK
    J Mol Biol 294:527-35. 1999
    ..Elements of both the protein and the nucleotide cofactor play important roles in triclosan recognition, providing an explanation for the factors controlling its tight binding to the enzyme and for the emergence of triclosan resistance...
  12. ncbi request reprint Crystallization of the dI component of transhydrogenase, a proton-translocating membrane protein
    S E Sedelnikova
    The Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 56:1170-2. 2000
    ..A full structure determination will lead to important information on the mode of action of this proton pump and will permit the comparison of the structure-function relationships of dI with those of alanine dehydrogenase...
  13. ncbi request reprint The crystal structure of Thermotoga maritima maltosyltransferase and its implications for the molecular basis of the novel transfer specificity
    A Roujeinikova
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN, England
    J Mol Biol 312:119-31. 2001
    ....
  14. pmc Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus
    P M Leonard
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
    EMBO J 20:990-7. 2001
    ..A possible location for an effector binding site is proposed by using sequence comparisons with other members of the family coupled to mutational analysis...
  15. ncbi request reprint Crystallization and preliminary X-ray analysis of Citrobacter amalonaticus methylaspartate ammonia lyase
    C W Levy
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:1922-4. 2001
    ....
  16. ncbi request reprint Purification, crystallization and quaternary structure analysis of a glycerol dehydrogenase S305C mutant from Bacillus stearothermophilus
    J Burke
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:165-7. 2001
    ..8 A resolution on a synchrotron-radiation source. Determination of the structure will provide insights into the key determinations of catalytic activity of this class of enzymes, for which no structures are currently available...
  17. ncbi request reprint Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase
    C W Levy
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
    Structure 10:105-13. 2002
    ..This analysis resolves the conflict that had linked MAL to the histidine and phenylalanine ammonia lyase family of enzymes...
  18. ncbi request reprint Crystallization and preliminary X-ray analysis of the ytxM gene product from Bacillus subtilis
    M M Mehanni
    The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 58:2138-40. 2002
    ..This crystal belongs to the primitive orthorhombic system, with approximate unit-cell parameters a = 44.3, b = 90.9, c = 136.1 A, alpha = beta = gamma = 90 degrees and two monomers in the asymmetric unit...
  19. pmc The catalytic role of aspartate in the active site of glutamate dehydrogenase
    J L Dean
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, U K
    Biochem J 301:13-6. 1994
    ..The data are entirely consistent with the direct involvement of D165 in catalysis rather than in the binding of coenzyme or 2-oxoglutarate...
  20. ncbi request reprint Crystal structure and active site location of N-(1-D-carboxylethyl)-L-norvaline dehydrogenase
    K L Britton
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, UK
    Nat Struct Biol 5:593-601. 1998
    ..The pattern of sequence conservation and substitution between members of this enzyme family has permitted the tentative location of the residues that define their differential substrate specificities...
  21. ncbi request reprint Crystallization and preliminary X-ray analysis of the glycerol-3-phosphate 1-acyltransferase from squash (Cucurbita moschata)
    A P Turnbull
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Western Bank, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:451-3. 2001
    ..1, b = 65.1, c = 103.3 A, alpha = beta = gamma = 90 degrees and a monomer in the asymmetric unit. X-ray diffraction data to 1.9 A resolution have been collected in-house using a MAR 345 imaging-plate system...
  22. ncbi request reprint Cloning, purification, crystallization and preliminary crystallographic analysis of Bacillus subtilis LuxS
    S K Das
    The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:1324-5. 2001
    ..55 A resolution on a synchrotron-radiation source. Determination of the structure will provide insights into the key determinants of function of this class of proteins, for which no structures are currently available...
  23. ncbi request reprint Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution
    P D Hempstead
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, England
    J Mol Biol 268:424-48. 1997
    ..L chains contain a group of glutamates associated with mineralisation within the iron storage cavity of the protein...
  24. ncbi request reprint Insights into thermal stability from a comparison of the glutamate dehydrogenases from Pyrococcus furiosus and Thermococcus litoralis
    K L Britton
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, England
    Eur J Biochem 229:688-95. 1995
    ..One hot spot for the accumulation of exchanges lies close to a region of the molecule involved in its conformational flexibility and these changes may modulate the dynamics of this enzyme and thereby contribute to increased stability...
  25. ncbi request reprint The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue
    T A Muranova
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, England
    Acta Crystallogr D Biol Crystallogr 57:1192-5. 2001
    ..1 and 1.2 A and are suitable for structural studies. The determination of these structures could be important in understanding the different catalytic power of each of these related catalytic antibodies...
  26. ncbi request reprint Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase
    P J Baker
    The Krebs Institute, The Department of Molecular Biology and Biotechnology, The University of Sheffield, UK
    Nat Struct Biol 5:561-7. 1998
    ..However, they are arranged differently on the enzyme surface, which has the effect of directing opposite faces of the keto acid to the dinucleotide in each case, forcing a change in absolute configuration of the product...
  27. ncbi request reprint Protein-protein recognition, hydride transfer and proton pumping in the transhydrogenase complex
    P A Buckley
    Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, UK
    Structure 8:809-15. 2000
    ..Transhydrogenase is a conformationally coupled proton pump linking a proton gradient to the redox reaction between NAD(H) and NADP(H). The enzyme has three components; dI binds NAD(H), dII spans the membrane and dIII binds NADP(H)...
  28. ncbi request reprint Crystallization and preliminary X-ray crystallographic studies on 4-alpha-glucanotransferase from Thermotoga maritima
    A Roujeinikova
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, England
    Acta Crystallogr D Biol Crystallogr 57:1046-7. 2001
    ..A complete data set has been collected to 2.6 A resolution using cryocooling conditions and synchrotron radiation. The crystals belong to space group I222 or I2(1)2(1)2(1), with unit-cell parameters a = 92.6, b = 180.3, c = 199.2 A...
  29. ncbi request reprint Use of chemical modification in the crystallization of isocitrate lyase from Escherichia coli
    S I Abeysinghe
    Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, U K
    J Mol Biol 220:13-6. 1991
    ..Considerations of the values of Vm and measurements on the crystal density indicate that the asymmetric unit of both crystals contains four subunits...
  30. ncbi request reprint Structural relationship between glutathione reductase and lipoamide dehydrogenase
    D W Rice
    J Mol Biol 174:483-96. 1984
    ..A divergent evolutionary relationship between the two enzymes including their NAD and NADP binding domains is fully supported by this analysis...
  31. pmc Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor
    J M Clements
    British Biotech Pharmaceuticals Ltd, Oxford OX4 6LY, United Kingdom
    Antimicrob Agents Chemother 45:563-70. 2001
    ..aureus protected mice from infection with median effective doses of 8 and 14 mg/kg of body weight, respectively. These data validate PDF as a novel target for the design of a new generation of antibacterial agents...
  32. ncbi request reprint Molecular basis of triclosan activity
    C W Levy
    Nature 398:383-4. 1999
  33. ncbi request reprint Molecular genetic analysis of enoyl-acyl carrier protein reductase inhibition by diazaborine
    G J de Boer
    Department of Genetics, Vrije Universiteit, HV Amsterdam, The Netherlands
    Mol Microbiol 31:443-50. 1999
    ..Larger amino acid side-chains, such as that of arginine, histidine, lysine and glutamine, completely inactivated the activity of the enzyme...
  34. pmc Delivery of antimicrobials into parasites
    B U Samuel
    Department of Visual Sciences, University of Chicago, 5841 South Maryland, AMB S 208, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 100:14281-6. 2003
    ....
  35. ncbi request reprint Fatty acid and sterol metabolism: potential antimicrobial targets in apicomplexan and trypanosomatid parasitic protozoa
    C W Roberts
    Department of Immunology, Strathclyde Institute for Biomedical Sciences, University of Strathclyde, Glasgow G4 ONR, Scotland, UK
    Mol Biochem Parasitol 126:129-42. 2003
    ..These properties may permit the parasites to evade treatment with sterol biosynthesis inhibitors in some clinical situations and need to be taken into account in the design of future drugs...
  36. ncbi request reprint Structure of human lactoferrin: crystallographic structure analysis and refinement at 2.8 A resolution
    B F Anderson
    Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand
    J Mol Biol 209:711-34. 1989
    ..Interdomain and interlobe interactions, the roles of charged side-chains, heavy-atom binding sites, and the construction of the metal site in relation to the binding of different metals are also discussed...
  37. ncbi request reprint Homology between CAP and Fnr, a regulator of anaerobic respiration in Escherichia coli
    D J Shaw
    J Mol Biol 166:241-7. 1983
    ..These homologies suggest that Fnr and CAP may have similar three-dimensional structures and that the regulation of anaerobic energy metabolism may involve interaction between Fnr and an unidentified effector molecule...
  38. ncbi request reprint Analysis of the structure, substrate specificity, and mechanism of squash glycerol-3-phosphate (1)-acyltransferase
    A P Turnbull
    The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN, Sheffield, United Kingdom
    Structure 9:347-53. 2001
    ....
  39. ncbi request reprint Contribution of an aspartate residue, D114, in the active site of clostridial glutamate dehydrogenase to the enzyme's unusual pH dependence
    S Coughlan
    Department of Biochemistry and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
    Biochim Biophys Acta 1544:10-7. 2001
    ....
  40. pmc Type I and type II fatty acid biosynthesis in Eimeria tenella: enoyl reductase activity and structure
    J Z Lu
    Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
    Parasitology 134:1949-62. 2007
    ..Interestingly, we also identified sequences that appear to encode multifunctional type I FAS enzymes, a feature also observed in Toxoplasma gondii, highlighting the similarity between these apicomplexan parasites...