Enzymatic transition state poise and transition state analogues

Accounts of Chemical Research

Volumn 36, Issue 8, 2003, Pages 588-596

  Schramm, Vern L ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROFOLATE REDUCTASE; DNA GLYCOSYLTRANSFERASE; ENZYME; ENZYME INHIBITOR; ISOENZYME; NUCLEOSIDASE;

CHEMICAL BINDING; CHEMICAL REACTION; CHEMICAL STRUCTURE; CORRELATION ANALYSIS; DISSOCIATION; ENZYME ANALYSIS; ENZYME KINETICS; ENZYME MECHANISM; ENZYME SPECIFICITY; IONIC STRENGTH; ISOTOPE LABELING; MATHEMATICAL COMPUTING; PHASE TRANSITION; REACTION ANALYSIS; REVIEW; STRUCTURE ANALYSIS; TRANSITION STATE POISE;

ANIMALS; CATALYSIS; CATALYTIC DOMAIN; ENZYME INHIBITORS; ENZYMES; KINETICS; THERMODYNAMICS;

EID: 0041472499     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar0200495     Document Type: Review

References (58)

1. Melander, L.; Saunders, W. J., Jr. Reaction Rates of Isotopic Molecules; John Wiley and Sons: New York, 1980; pp 4-55.
2. Cleland, W. W., O'Leary, M. H., Northrop, D. B., Eds. In Isotope Effects on Enzyme-Catalyzed Reactions; University Park Press: Baltimore, 1977.
3. Northrop, D. B. The expression of isotope effects on enzyme-catalyzed reactions. Annu. Rev. Biochem. 1981, 50, 103-131.
4. Cook, P. F., Ed. In Enzyme Mechanism From Isotope effects; CRC Press: Boca Raton, FL, 1991.
5. Sims, L. B.; Lewis, D. E. Bond order methods for calculating isotope effects in organic reactions. In Isotopes in Organic; Buncel, E., Lee, C. C., Eds.; Elsevier: New York, 1984; Chemistry Vol. 6, pp 161-259.
6. Huskey, W. P. Model calculations of isotope effects using structures containing low-barrier hydrogen bonds. J. Am. Chem. Soc. 1996, 118, 1663-1668.
7. Anisimov, V.; Paneth, P. ISOEFF98. A program for studies of isotope effects using Hessian modifications. J. Mater. Chem. 1999, 26, 75-86.
8. +, J. Am. Chem. Soc. 1997, 119, 12069-12078.
9. Berti, P. J. Determining transition states from kinetic isotope effects. Methods Enzymol. 1999, 308, 355-397.
10. + with the specific incorporation of atomic labels. J. Am. Chem. Soc. 1994, 116, 6531-6536.
11. 3H kinetic isotope effects on acid-catalyzed glycosidic bond hydrolysis of AMP, dAMP and inosine. J. Biol. Chem. 1984, 259, 9411-9417.
12. + catalyzed by diphtheria toxin. J. Am. Chem. Soc. 1997, 119, 12079-12088.
13. 18O]oxamate with NADH and lactate dehydrogenase. Biochemistry 1995, 34, 6050-6058.
14. Keating, A. E.; Merrigan, S. R.; Singleton, D. A.; Houk, K. N. Experimental proof of the nonleast-motion cycloadditions of dichlorocarbene to alkenes: Kinetic isotope effects and quantum mechanical transition states. J. Am. Chem Soc. 1999, 121, 3933-3938
15. Smith, L. E. H., Mohr, L. H.; Raftery, M. A. Mechanisms for lysozyme-catalyzed hydrolysis. J. Am. Chem. Soc. 1973, 95, 7497.
16. Rodgers, J.; Femec, D. A.; Schowen, R. L. Isotopic mapping of transition-state structural features associated with enzymatic catalysis of methyl transfer. J. Am. Chem. Soc. 1982, 104, 3263.
17. Sicinska, D.; Truhlar, D. G.; Paneth, P.; Solvent-dependent transition states for decarboxylations. J. Am. Chem. Soc. 2001, 123, 7683-7686.
18. Bruice, T. C.; Lightstone, F. C. Ground state and transition state contributions to the rates of intramolecular and enzymatic reactions. Acc. Chem. Res. 1999, 32, 127-136
19. Matthews, D. A.; Bolin, J. T.; Burridge, J. M.; Filman, D. J.; Volz, K. W., Kaufman, B. T.; Beddell, C. R.; Champress, J. N., Stammers, D. K.; Kraut, J. Dihydrofolate reductase. The stereochemistry of inhibitor selectivity. J. Biol. Chem. 1985, 260, 381-391.
20. Merkler, D. J.; Kline, P. C., Weiss, P.; Schramm, V. L. Transition state analysis of AMP deaminase. Biochemistry 1993, 32, 12993-13001.
21. Lewandowicz, A.; Rudzinski, J.; Luo, L.; Dunaway-Mariano, D.; Paneth, P. Determination of the chlorine kinetic isotope effect on the 4-chlorobenzoyl-CoA dehalogenase-catalyzed nucleophillc aromatic substitution. Arch. Biochem. Biophys. 2002, 398, 249-252.
22. Chen, X.-Y.; Link, T. M.; Schramm, V. L. Inhibition of ricin by an RNA stem-loop containing a rib-oxycarbonium mimic. J. Am. Chem. Soc. 1996, 118, 3067-3068.
23. Chen, X.-Y.; Berti, P. J.; Schramm, V. L. Transition state structure for depurination of DNA by ricin A-chain. J. Am. Chem. Soc. 2000, 122, 6527-6534.
24. Werner, R. M.; Stivers, J. T. Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: Evidence for an oxocarbenium ion-uracil anion intermediate. Biochemistry 2000, 39, 14054-14064.
25. Amyes, T. L.; Jencks, W. P. Lifetimes of oxocarbenium ions in aqueous solution from common ion inhibition of the solvolysis of.alpha.-azido ethers by added azide ion. J. Am. Chem. Soc. 1989, 111, 7888-7900.
26. Parikh, S. S.; Walcher, G.; Jones, G. D.; Slupphaug, G.; Krokan, H. E.; Blackburn, G. M.; Tainer, J. A. Uracil-DNA glycosylase-DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Proc. Nat. Acad. Sci. U.S.A. 2000, 97, 5083-5088.
27. Chen, X.-Y.; Link, T. M.; Schramm, V. L. Ricin A-chain: kinetics, mechanism and RNA-stem-loop inhibitors. Biochemistry 1998, 37, 11605-11613.
28. Tanaka, K. S. E.; Chen, X.-Y.; Ichikawa, Y.; Tyler, P. C.; Furneaux, R. H.; Schramm, V. L. Ricin A-chain inhibitors resembling the oxacarbenium ion transition state. Biochemistry 2001, 40, 6845-6851.
29. Kati, W. M.; Acheson, S. A.; Wolfenden, R. A transition state in pieces: major contributions of entropic effects to ligand binding by adenosine deaminase. Biochemistry 1992, 31, 7356-7366.
30. Mazzella, L. J.; Parkin, D. W.; Tyler, P. C.; Furneaux, R. H.; Schramm, V. L. Mechanistic diagnoses of N-ribohydrolases and purine nucleoside phosphorylase. J. Am. Chem. Soc. 1996, 118, 2111-2112.
31. Jiang, Y. L.; Stivers, J. T. Mutational analysis of the base-flipping mechanism of uracil DNA glycosylase. Biochemistry 2002, 41, 11236-11247.
32. Jiang, Y. L.; Ichikawa, Y.; Stivers, J. T. Inhibition of uracil DNA glycosylase by an oxacarbenium ion mimic. Biochemistry 2002, 41, 7116-7124.
33. Parkin, D. W.; Horenstein, B. A.; Abdulah, D. R.; Estupinan, B.; Schramm, V. L. Nucleoside hydrolase from Crithidia fasciculata. Metabolic role, purification, specificity, and kinetic mechanism. J. Biol. Chem. 1991, 266, 20658-20665.
34. Dai, Y.; Pochapsky, T. C.; Abeles, R. H. Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae. Biochemistry 2001, 40, 6379-6387.
35. Winzer, K.; Hardie, K. R.; Burgess, N.; Doherty, N.; Kirke, D.; Golden, M. T. G.; Linforth, R.; Cornell, K. A.; Taylor, A. J.; Hill, P. J.; Williams, P.; Lux, S. its role in central metabolism and the in vitro synthesis of 4-hydroxy-5-methyl-3(2H)-furanone. Microbiology 2002, 148, 909-922.
36. Horenstein, B. A.; Parkin, D. W.; Estupinan, B.; Schramm, V. L. Transition state analysis of nucleoside hydrolase from Crithidia fasciculata. Biochemistry 1991, 30, 10788-10795.
37. Parkin, D. W.; Limberg, G.; Tyler, P. C.; Furneaux, R. H.; Chen, X.-Y.; Schramm, V. L. Isozyme-specific transition state inhibitors for the trypanosomal nucleoside hydrolases. Biochemistry 1997, 36, 3528-3534.
38. Parkin, D. W. Purine-specific nucleoside N-ribohydroase from Trypanosoma brucei brucei. J. Biol. Chem. 1996, 271, 21713-21719.
39. Giblett, E. R.; Ammann, A. J.; Wara, D. W.; Sandman, R.; and Diamond, L. K. Nucleoside-phosphorylase deficiency in a child with severely defective T-cell immunity and normal B-cell immunity. Lancet 1975, 1, 1010-1013.
40. Kicska, G. A.; Long, L.; Hörig, H.; Fairchild, C.; Tyler, P. C.; Furneaux, R. H.; Schramm, V. L.; Kaufman, H. L. Immucillin-H a powerful transition state analogue inhibitor of purine nucleoside phosphorylase, selectively inhibits human T-lymphocytes. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 4593-4598.
41. Kline, P. C.; Schramm, V. L. Purine nucleoside phosphorylase. Catalytic mechanism and transition state analysis of the arsenolysis reaction. Biochemistry 1993, 32, 13212-13219.
42. Kline, P. C.; Schramm, V. L. Purine nucleoside phosphorylase. Inosine hydrolysis, tight binding of the hypoxanthine intermediate and third-the-sites reactivity. Biochemistry 1992, 31, 5964-5973.
43. Miles, R. W.; Tyler, P. C.; Furneaux, R. H.; Bagdassarian, C. K.; Schramm, V. L. One-third-the-sites transition state inhibitors for purine nucleoside phosphorylase. Biochemistry 1998, 37, 8615-8621.
44. Fedorov, A.; Shi, W.; Kicska, G.; Fedorov, E.; Tyler, P. C.; Furneaux, R. H.; Hanson, J. C.; Gainsford, G. J.; Larese, J. Z.; Schramm, V. L.; Almo, S. C. Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis. Biochemistry 2001, 40, 853-860.
45. Garrett, E. R.; Mehta, P. J. Solvolysis of adenine nucleosides. I. Effects of sugars and adenine substituents on acid solvolysis. J. Am. Chem. Soc. 1972, 94, 8532-8541.
46. McCarter, J. D.; Withers, S. G. Mechanisms of enzymatic glycoside hydrolysis. Curr. Opin. Struct. Biol. 1994, 4, 885-892.
47. Vocadlo, D. J.; Davies, G. J.; Laine, R.; Withers, S. G. Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate. Nature 2001, 412, 835-838.
48. Kicska, G. A.; Tyler, P. C.; Evans, G. B.; Furneaux, R. H.; Shi, W.; Fedorov, A., Lewandowicz, A.; Cahill, S. M.; Almo, S. C.; Schramm, V. L. Atomic dissection of the hydrogen bond network for transition state analogue binding to purine nucleoside phosphorylase. Biochemistry 2002, 41, 14489-14498.
49. Mazumder, D.; Bruice, T. C. Exploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzyme-bound substrate and transition state. J. Am. Chem. Soc. 2002, 124, 14591-14600.
50. Sauve, A. A.; Cahill, S. M.; Zech, S. G.; Basso, L. A.; Santos, D. S.; Grubmeyer, C.; Evans, G. B.; Furneaux, R. H.; Tyler, P. C.; McDermott, A.; Girvin, M. E.; Schramm, V. L. Ionic states of substrates and transition state analogues at the catalytic sites of N-ribosyltransferases. Biochemistry 2003, in press.
51. Scheuring, J.; Schramm, V. L. Kinetic isotope effect characterization of the transition state for oxidized nicotinamide adenine dinucleotide hydrolysis by pertussis toxin. Biochemistry 1997, 36, 4526-4534.
52. Scheuring, J.; Schramm, V. L. Pertussis toxin: transition state analysis for ADP-ribosylation of G-protein peptide αi3C20. Biochemistry 1997, 36, 8215-8223.
53. iα1 subunits by pertussis toxin. Biochemistry 1998, 37, 2746-2758.
54. Markham, G. D.; Parkin, D. W.; Mentch, F.; Schramm, V. L. A kinetic isotope effect study and transition state analysis of the S-adenosylmethionine synthetase reaction. J. Biol. Chem. 1987, 262, 5609-5615.
55. Lewandowicz, A.; Sicinska, D.; Rudzinski, J.; Ichiyama, S.; Kurihara, T. ; Esaki, N.; Paneth, P. Chlorine kinetic isotope effect on the fluoroacetate dehalogenase reaction. J. Am. Chem. Soc. 2001, 123, 9192-9193.
56. Lewandowicz, A.; Rudzinski, J.; Tronstad, L.; Widersten, M.; Ryberg, P.; Matsson, O.; Paneth, P. Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction. J. Am. Chem. Soc. 2001, 123, 4550-4555.
57. Schramm, V. L. Enzymatic transition-state analysis and transition-state analogues. Methods Enzymol. 1999, 308, 301-355.
58. Lewandowicz, A.; Shi, W.; Evans, G. B.; Tyler, P. C.; Furneaux, R. H.; Basso, L. A.; Santos, D. S.; Almo, S. C.; Schramm, V. L. Overthe-barrier transition state analogues and crystal structure with Mycobacterium tuberculosis purine nucleoside phosphorylase. Biochemistry, in press.