Kinetic isotope effects of nucleoside hydrolase from Escherichia coli

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1751, Issue 2, 2005, Pages 140-149

  Hunt, Cindy ^a   Gillani, Niloufar ^a   Farone, Anthony ^a   Rezaei, Mansoureh ^a   Kline, Paul C ^a  

^a MIDDLE TENNESSEE STATE UNIVERSITY   (United States)

Author keywords

Kinetic isotope effect; Nucleoside hydrolase; Transition state

Indexed keywords

CARBON 13; DEUTERIUM; NITROGEN 15; NUCLEOSIDASE; OXYGEN; URIDINE;

ARTICLE; BACTERIAL KINETICS; CATALYSIS; CHEMICAL BOND; CHEMICAL REACTION KINETICS; CRITHIDIA FASCICULATA; ENZYME ISOLATION; ENZYME MECHANISM; ESCHERICHIA COLI; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYDROGEN BOND; ISOTOPE ANALYSIS; ISOTOPE LABELING; MASS SPECTROMETRY; PHASE TRANSITION; PRIORITY JOURNAL; PROKARYOTE; PROTEIN CONFORMATION; PROTEIN FAMILY; PROTEIN HYDROLYSIS; PROTON TRANSPORT;

AMINO ACID SEQUENCE; ANIMALS; CARBON ISOTOPES; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CRITHIDIA FASCICULATA; DEUTERIUM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; ISOTOPES; KINETICS; MASS SPECTROMETRY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; N-GLYCOSYL HYDROLASES; NITROGEN ISOTOPES; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; URIDINE;

CRITHIDIA FASCICULATA; ESCHERICHIA COLI; PROKARYOTA;

EID: 23444460570     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2005.06.001     Document Type: Article

References (46)

1. C. Petersen, and L.B. Møller The rihA, rihB, and rihC ribonucleoside hydrolases of Escherichia coli J. Biol. Chem. 276 2001 884 894
2. B. Estupiñán, and V.L. Schramm Guanosine-inosine-preferring nucleoside N-glycohydrolase from Crithidia fasciculata J. Biol. Chem. 269 1994 23068 23073
3. D.W. Parkin, B.A. Horenstein, D.R. Abdulah, B. Estupiñán, and V.L. Schramm Nucleoside hydrolase from Crithidia fasciculata J. Biol. Chem. 266 1991 20658 20665
4. W. Shi, V.L. Schramm, and S.C. Almo Nucleoside hydrolase from Leishmania major J. Biol. Chem. 274 1999 21114 21120
5. G. Magni, E. Fioretti, P.L. Ipata, and P. Natalini Bakers' yeast uridine nucleosidase. Purification, composition, and physical and enzymic properties J. Biol. Chem. 250 1975 9 13
6. A. Bzowska, E. Kulikowska, and D. Shugar Purine nucleoside phosphorylase: properties, functions, and clinical aspects Pharmacol. Ther. 88 2000 349 425
7. B.A. Horenstein, and V.L. Schramm Correlation of the molecular electrostatic potential surface of an enzymic transition state with novel transition-state inhibitors Biochemistry 32 1993 9917 9925
8. C.F. Beck, and J.L. Ingraham Location on the chromosome of Salmonella typhimurium of genes governing pyrimidine metabolism Mol. Gen. Genet. 111 1971 303 316
9. P. Valentin-Hansen Uridine-cytidine kinase from Escherichia coli P.A. Hoffee M.E. Jones Purine and Pyrimidine Nucleotide Metabolism Methods in Enzymology vol. 51 1978 Academic Press New York 308 314
10. C. Petersen Inhibition of cellular growth by increased guanine nucleotide pools. Characterization of an Escherichia coli mutant with a guanosine kinase that is insensitive to feedback inhibition by GTP J. Biol. Chem. 274 1999 5348 5356
11. B.A. Horenstein, D.W. Parkin, B. Estupiñán, and V.L. Schramm Transition-state analysis of nucleoside hydrolase from Crithidia fasciculata Biochemistry 30 1991 10788 10795
12. M. Degano, D.N. Gopaul, G. Scapin, V.L. Schramm, and J.C. Sacchettini Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata Biochemistry 35 1996 5971 5981
13. D.N. Gopaul, S.L. Meyer, M. Degano, J.C. Sacchettini, and V.L. Schramm Inosine-uridine nucleoside hydrolase from Crithidia fasciculata. Genetic characterization, crystallization, and identification of histidine 241 as a catalytic site residue Biochemistry 35 1996 5963 5970
14. M. Degano, S.C. Almo, J.C. Sacchettini, and V.L. Schramm Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor Biochemistry 37 1998 6277 6285
15. L.J. Mazzella, D.W. Parkin, P.C. Tyler, R.H. Furneaux, and V.L. Schramm Mechanistic diagnoses of N-ribohydrolases and purine nucleoside phosphorylase J. Am. Chem. Soc. 118 1996 2111 2112
16. V.L. Schramm, B.A. Horenstein, and P.C. Kline Transition state analysis and inhibitor design for enzymatic reactions J. Biol. Chem. 269 1994 18259 18262
17. G. Cook, and M. Greenberg A general synthesis of C2′-deuterated ribonucleosides J. Org. Chem. 59 1994 4704 4706
18. 13C] uridine. An efficient, regiospecific synthesis of the pyrimidine ring J. Org. Chem. 43 1978 1547 1550
19. H. Vorbrüggen, K. Kroliliewicz, and B. Bennua Nucleoside syntheses: XXII. Nucleoside synthesis with trimethylsilyl triflate and perchlorate as catalysts Chem. Ber. 114 1981 1234 1255
20. 13C spin-coupling constants to assess furanose and N-glycoside bond conformations J. Am. Chem. Soc. 112 1990 7373 7381
21. D.C. Baker, and T.H. Haskell Synthesis of tritium- and deuterium-labeled 9-β-d-arabinofuranosyoladenine and the tritium-labeled 5′- monophosphate ester with increased metabolic stability J. Med. Chem. 18 1975 1041 1044
22. + catalyzed by diphtheria toxin J. Am. Chem. Soc. 119 1997 12079 12088
23. L.B. Sims, G.W. Burton, and D.E. Lewis Quantum Chemistry Program Exchange vol. 337 1977 Indiana University Bloomington, IN
24. L.B. Sims, and D.E. Lewis Bond order methods for calculating isotope effects in organic reactions E. Buncel C.C. Lee Isotopes in Organic Chemistry vol. 6 1984 Elsevier Science New York 161 259
25. E.A. Green, R.D. Rosenstein, R. Shiono, D.J. Abraham, B.L. Trus, and R.E. Marsh The crystal structure of uridine Acta Crystallogr. B31 1975 102 107
26. V.L. Schramm Kinetic isotope effects for hydrolase reactions P.F. Cook Enzyme Mechanism from Isotope Effects 1991 CRC Press Boca Raton, FL 367 388
27. P.C. Kline, M. Rezaee, and T.A. Lee Determination of kinetic isotope effects for nucleoside hydrolases using gas chromatography/mass spectrometry Anal. Biochem. 275 1999 6 10
28. L. Melander, and W.H. Saunders Jr. Reaction Rates of Isotopic Molecules 1980 Wiley and Sons New York 74 75
29. C.G. Swain, E.C. Stivers, J.F. Reuwer, and L.J. Schaad Use of hydrogen isotope effects to identify the attacking nucleophile in the enolization of ketones catalyzed by acetic acid J. Am. Chem. Soc. 80 1958 5885 5893
30. X.-Y. Chen, P.J. Berti, and V.L. Schramm Transition-state analysis for depurination of DNA by ricin A-chain J. Am. Chem. Soc. 122 2000 6527 6534
31. J.J. Prior, and D.V. Santi On the mechanism of the acid-catalyzed hydrolysis of uridine to uracil J. Biol. Chem. 259 1984 2429 2434
32. 3H kinetic isotope effects on acid-catalyzed glycosidic bond hydrolysis of AMP, dAMP, and inosine J. Biol. Chem. 259 1984 9411 9417
33. V.L. Schramm Enzymatic transition states and transition state analog design C.C. Richardson J.N. Abelson C.H. Raetz J.W. Thorner Annual Review of Biochemistry vol. 67 1998 Annual Reviews Palo Alto CA 693 720
34. B. Capon Mechanism in carbohydrate chemistry Chem. Rev. 69 1969 449 454
35. R. Shapiro, and M. Danzig Acidic hydrolysis of deoxycytidine and deoxyuridine derivatives. The general mechanism of deoxyribonucleoside hydrolysis Biochemistry 11 1972 23 29
36. C.D. Poulter, and G.D. Fredrick Uracil and its 4-hydroxy-1(H) and 2-hydroxy 3(H) protomers. pKa's and equilibrium constants Tetrahedron Lett. 26 1975 2171 2174
37. T. Ellenberger Pocketing the difference: structures of uracil excision repair proteins Chem. Biol. 2 1995 351 354
38. G. Slupphaug, C.D. Mol, B. Kavli, A.S. Arvai, H.E. Krokan, and J.A. Tainer A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA Nature 384 1996 87 92
39. W. Versées, and J. Steyaert Catalysis by nucleoside hydrolase Curr. Opin. Struct. Biol. 13 2003 731 738
40. A.C. Drohat, J. Jagadeesh, E. Ferguson, and J.T. Stivers Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase Biochemistry 38 1999 11866 11875
41. A.C. Drohat, G. Xiao, M. Tordova, J. Jagadeesh, K.W. Pankiewica, K.A. Watanabe, G.L. Gilliland, and J.T. Stivers Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187 Biochemistry 38 1999 11876 11886
42. R.M. Werner, and J.T. Stivers Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate Biochemistry 39 2000 14054 14064
43. S.S. David, and S.D. Williams Chemistry of glycosylases and endonucleases involved in base-excision repair Chem. Rev. 98 1998 1221 1261
44. M.R. Walter, W.J. Cook, L.B. Cole, S.A. Short, G.W. Koszalka, T.A. Krenitsky, and S.E. Ealick Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 Å resolution J. Biol. Chem. 265 1990 14016 14022
45. M.R. Birck, and V.L. Schramm Nucleophilic participation in the transition state for human thymidine phosphorylase J. Am. Chem. Soc. 126 2004 2447 2453
46. N. Gillani, Site-directed mutagenesis of inosine-uridine hydrolase in Escherichia coli. M.S. Thesis, Middle Tennessee State University Murfreesboro, TN 2002.