Toward a structural understanding of the dehydratase mechanism

Structure

Volumn 10, Issue 1, 2002, Pages 81-92

  Allard, Simon T M ^a   Beis, Konstantinos ^a   Giraud, Marie France ^a   Hegeman, Adrian D ^b   Gross, Jeffrey W ^b   Wilmouth, Rupert C ^c   Whitfield, Chris ^d   Graninger, Michael ^e   Messner, Paul ^e   Allen, Andrew G ^f   Maskell, Duncan J ^f   Naismith, James H ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF GUELPH   (Canada)

^e UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

^f UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Crystallography; Dehydratase; dTDP D glucose 4,6 dehydratase; L rhamnose; Mechanism; RmlB

Indexed keywords

ASPARTIC ACID; DEOXYTHYMIDINE 5' DIPHOSPHATE DEXTRO GLUCOSE 4,6 DEHYDRATASE; GLUCOSE; GLUTAMIC ACID; HYDROLYASE; RHAMNOSE; THYMIDINE DIPHOSPHATE; TYROSINE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DEHYDRATION; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME METABOLISM; NONHUMAN; PRIORITY JOURNAL; SALMONELLA ENTERICA; SEROTYPE; STREPTOCOCCUS SUIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; GLUCOSE; HYDRO-LYASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN STRUCTURE, TERTIARY; SALMONELLA TYPHIMURIUM; SEQUENCE ALIGNMENT; STREPTOCOCCUS SUIS;

NEGIBACTERIA; POSIBACTERIA; SALMONELLA; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM; STREPTOCOCCUS; STREPTOCOCCUS SUIS;

EID: 0036151285     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(01)00694-3     Document Type: Article

References (67)

1. The enzymatic synthesis of thymidine-linked sugars
2. The rhamnose pathway
3. Chemical and biochemical aspects of deoxysugars and deoxysugar oligosaccharides
4. Characterization of dTDP-4-dehydrorhamnose 3,5-epimerase and dTDP-4-dehydrorhamnose reductase, required for dTDP-L-rhamnose biosynthesis in Salmonella enterica serovar Typhimurium LT2
5. Surface layer glycoproteins of bacteria and archaea
6. Drug targeting Mycobacterium tuberculosis cell wall synthesis: Genetics of dTDP-rhamnose synthetic enzymes and development of a microtiter plate-based screen for inhibitors of conversion of dTDP-glucose to dTDP-rhamnose
7. The type-specific polysaccharides of Streptococcus suis
8. Structure of lipopolysaccharides from gram-negative bacteria. III. Structure of O-specific polysaccharides
9. Identification and characterization of the cps locus of Streptococcus suis serotype 2: The capsule protects against phagocytosis and is an important virulence factor
10. The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA)
11. The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-L-rhamnose pathway
12. RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase
13. Overexpression, purification, crystallization and preliminary structural study of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD), the fourth enzyme of the dTDP-L-rhamnose synthesis pathway, from Salmonella enterica serovar Typhimurium
14. Mechanisms and pathways from recent deoxysugar biosynthesis research
15. Novel enzymatic mechanisms in carbohydrate metabolism
16. Pathways and mechanisms in the biogenesis of novel deoxysugars by bacteria
17. Mechanistic roles of Thr134, Tyr160, and Lys164 in the reaction catalyzed by dTDP-glucose 4,6-dehydratase
18. Probing catalysis by Escherichia coli dTDP-glucose-4,6-dehydratase: Identification and preliminary characterization of functional amino acid residues at the active site
19. Characterization of enzymatic processes by rapid mix-quench mass spectrometry: The case of dTDP-glucose 4,6-dehydratase
20. Biological mechanisms involved in the formation of deoxy sugars. IV. Enzymatic conversion of thymidine diphosphoglucose-4T to thymidine diphospho-4-keto-6-deoxyglucose-6T
21. Acid-base catalysis by UDP-galactose 4-epimerase: Correlations of kinetically measured acid dissociation constants with thermodynamic values for tyrosine 149
22. High-resolution X-ray structure of UDP-galactose 4-epimerase complexed with UDP-phenol
23. Molecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: Implications for the catalytic mechanism
24. Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli
25. Molecular structures of the S124A, S124T, and S124V site-directed mutants of UDP-galactose 4-epimerase from Escherichia coli
26. Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli
27. Dramatic differences in the binding of UDP-galactose and UDP-glucose to UDP-galactose 4-epimerase from Escherichia coli
28. Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase
29. Human UDP-galactose 4-epimerase: Accommodation of UDP-N-acetylglucosamine within the active site
30. Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose
31. Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose
32. Short-chain dehydrogenases/reductases (SDR)
33. Site-specific mutagenesis of Drosophila alcohol dehydrogenase: Evidence for involvement of tyrosine-152 and lysine-156 in catalysis
34. Reversible changes of ordered polypeptide structures in oxidized and reduced epimerase
35. Uridine diphosphate galactose-4-epimerase. Uridine monophosphate-dependent reduction by alpha- and beta-D-glucose
36. The Leloir pathway: A mechanistic imperative for three enzymes to change the stereochemical configuration of a single carbon in galactose
37. Biosynthesis of deoxysugars
38. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase
39. The mechanism of 6-deoxyhexose synthesis IV. The role of pyridine nucleotide in substrate release
40. Biological mechanisms involved in the formation of deoxysugars. VI. Role and function of enzyme-bound nicotinamide adenine dinucleotide in thymidine diphosphate D-glucose oxidoreductase
41. Stereochemistry of the dTDP-glucose oxidoreductase reaction
42. Complex pyridine nucleotide-dependent transformations
43. Sugar nucleotide-modifying enzymes
44. The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: Catalysis with a twist
45. Flavoenzymes: Diverse catalysts with recurrent features
46. Low-barrier hydrogen bonds and enzymic catalysis
47. The low barrier hydrogen bond in enzymatic catalysis
48. Understanding enzyme-catalyzed proton abstraction from carbon acids: Details of stepwise mechanisms from β-elimination reactions
49. Dehydration is catalyzed by glutamate-136 and aspartic acid-135 active site residues in Escherichia coli dTDP-glucose 4,6-dehydratase
50. The purification, crystallization and structural elucidation of dTDP-D-glucose 4,6-dehydratase (RmlB), the second enzyme of the dTDP-L-rhamnose synthesis pathway from Salmonella enterica serovar typhimurium
51. Recent changes to the MOSFLM package for processing film and image plate data
52. The CCP4 suite: Programs for protein crystallography
53. AMoRe: An automated package for molecular replacement
54. Solvent content of protein crystals
55. Crystallography & NMR system: A new software suite for macromolecular structure determination
56. Improved methods for binding protein models in electron density maps and the location of errors in these models
57. Efficient anisotropic refinement of macromolecular structures using FFT
58. Automated protein model building combined with iterative structure refinement
59. Protein structure comparison by alignment of distance matrices
60. Procheck: A program to check the stereochemical quality of protein structures
61. WHAT IF: A molecular modeling and drug design program
62. PROMOTIF - A program to identify and analyze structural motifs in proteins
63. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
64. Detection, delineation, measurement and display of cavities in macromolecular structures
65. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions