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Volumn 129, Issue 22, 2007, Pages 7055-7064

Transition state analysis of acid-catalyzed dAMP hydrolysis

Author keywords

[No Author keywords available]

Indexed keywords

BOND CLEAVAGE; DEOXYADENOSINE MONOPHOSPHATE (DAMP); KINETIC ISOTOPE EFFECTS (KIE); TRANSITION STATE ANALYSIS;

EID: 34250201455     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja067371l     Document Type: Article
Times cited : (45)

References (109)
  • 1
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    • Abbreviations: α, β-Me-dRMP, α- or β-methyl deoxy-D-ribose-5′-monophosphate; APRTase, adenine phosphoribosyl transferase; CIPC. contact ion pair complex; cpm, counts per min; dAdo, deoxyadenosine; DFT, density functional theory; dRMP, deoxy-D-ribose- 5′-monophosphate; DTT, dithiothreitol; EIE, equilibrium isotope effect; f, fractional extent of reaction; KIE, kinetic isotope effect; MK, myokinase; MTAN, 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase; nij. Pauling bond order; PEP, phosphoenolpyruvate; PK, pyruvate kinase; PRPPase, phosphoribosyl pyrophosphate synthetase; Q,Q‡. reduced isotopic partition function; RTRase, ribonucleoside triphosphate reductase; SSIPC, solvent separated ion pair complex; TBAS, tetrabutylammonium hydrogen sulfate; TEAA, triethyl ammonium acetate; θH2′, dihedral angle of p-orbital-Cl′-C2′-H2
    • H2′, dihedral angle of p-orbital-Cl′-C2′-H2′; TP, thymidine phosphorylase; TS, transition state; UDG, uracil DNA glycosylase.
  • 31
    • 33845185675 scopus 로고    scopus 로고
    • Mechanisms are described with IUPAC nomenclature. A N represents nucleophilic association, and DN represents nucleofugic dissociation. A concerted, bimolecular (SN2) reaction is represented as ANDN. DN* AN and DN, AN mechanisms are stepwise S NI, with a discrete intermediate formed between leaving group departure and nucleophile approach. The signs * and, denote, respectively, an intermediate too short-lived for the leaving group to diffuse into solution and one that is diffusionally equilibrated with solvent. P indicates diffusional separation of the intermediate complex and is not normally written, unless it becomes kinetically significant. For stepwise mechanisms * indicates the kinetically significant transition state, if known. Guthrie, R. D, Jencks, W. P. Acc. Chem. Res. 1989
    • NI). with a discrete intermediate formed between leaving group departure and nucleophile approach. The signs "*" and "+" denote, respectively, an intermediate too short-lived for the leaving group to diffuse into solution and one that is diffusionally equilibrated with solvent. "P" indicates diffusional separation of the intermediate complex and is not normally written, unless it becomes kinetically significant. For stepwise mechanisms "*" indicates the kinetically significant transition state, if known. Guthrie, R. D.; Jencks, W. P. Acc. Chem. Res. 1989, 22, 343-349.
  • 32
    • 0032845061 scopus 로고    scopus 로고
    • For KIEs measured by the competitive method, as in this study, the kinetically significant step is the first irreversible step rather than the rate-limiting step (see refs 12, 19, and Berti, P. J. Methods Enzymol. 1999, 308, 355-397, The degree of irreversibility of a given step is determined by the partitioning of the product of that step. Thus, in Scheme 3, the reversibility of oxacarbenium ion formation is given by k5/k4 see eq 2
    • 4 (see eq 2).
  • 34
    • 33947465376 scopus 로고    scopus 로고
    • KIEs from other studies were converted to the same isotope and temperature as those used in this study. Other isotopes were converted using the Swain-Schaad relationship: 14C-KIE, 13C-KIE 1.89 and 3H-KIE, 2H-KIE1.44. Other temperatures, T, were converted to 30°C using KIE303K, exp[ln-(KIET) x (T/303, a) Swain, C. G, Stivers, E. C, Reuwer, J. F, Jr, Schaad, L. J. J. Am. Chem. Soc. 1958, 80, 5885-5893
    • T) x (T/303)]. (a) Swain, C. G.; Stivers, E. C.; Reuwer, J. F., Jr.; Schaad, L. J. J. Am. Chem. Soc. 1958, 80, 5885-5893.
  • 53
    • 34250217169 scopus 로고    scopus 로고
    • m/z, 411 corresponds to [2′S-2H]dATP. This arises because the 14C-labeled glucose contains an unlabeled carrier. It is not radioactive and, therefore, not visible by scintillation counting, m/z, 412 corresponds to [5′-14C]-dADP, plus natural abundance isotopes (mostly 13C) adding 1 to the m/z, 411 peak. The relative intensities in unlabeled dATP was I 411/I412, 1:0.21. Subtracting the contribution from natural abundance isotopes to the m/z, 412 peak, the ratio I412/I413 was 4:96. Thus, 96% of 14C-labeled dATP contained 2H, i.e, was [2′S-2H, 5′-14C]dATP
    • 14C]dATP.
  • 54
    • 0003855149 scopus 로고    scopus 로고
    • Ausubel, F. M, Smith, J. A, Moore, D. D, Brent, R, Seidman, J. C, Struhl, K, Kingston, R. E, Eds, Wiley: New York
    • Short Protocols in Molecular Biology; Ausubel, F. M., Smith, J. A., Moore, D. D., Brent, R., Seidman, J. C., Struhl, K., Kingston, R. E., Eds.; Wiley: New York, 1999.
    • (1999) Short Protocols in Molecular Biology
  • 58
    • 0004082237 scopus 로고
    • Cook, P. F, Ed, CRC Press, Inc, Boca Raton, FL
    • Parkin, D. W. In Enzyme mechanism from isotope effects; Cook, P. F., Ed.; CRC Press, Inc.: Boca Raton, FL, 1991; pp 269-290.
    • (1991) Enzyme mechanism from isotope effects , pp. 269-290
    • Parkin, D.W.1
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    • Frisch, M. J., et al. Gaussian 98; Gaussian, Inc.: Pittsburgh, PA, 1998.
    • (1998) Gaussian 98
    • Frisch, M.J.1
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    • 2O])/[dRMP][MeOH]. (a) Tashma, R.; Rappoport, Z. Adv. Phys. Org. Chem. 1992, 27, 239-291.
    • 2O])/[dRMP][MeOH]. (a) Tashma, R.; Rappoport, Z. Adv. Phys. Org. Chem. 1992, 27, 239-291.
  • 71
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    • a,N1H,N7H = -1-3 for diprotonation. (a) Remaud, G.; Zhou, X. X.; Chattopadhyaya, J.; Oivanen, M.; Lonnberg, H. Tetrahedron 1987, 43, 4453-4461.
    • a,N1H,N7H = -1-3 for diprotonation. (a) Remaud, G.; Zhou, X. X.; Chattopadhyaya, J.; Oivanen, M.; Lonnberg, H. Tetrahedron 1987, 43, 4453-4461.
  • 84
    • 34250183543 scopus 로고    scopus 로고
    • Furanosyl ring puckers are indicated with n-endo and n-exo designations, where all ring atoms except n are in the same plane. Atom n is displaced toward the 5′-substituent in n-endo conformers and away in n-exo. (a) Joint Commission on Biochemical Nomenclature. Pure Appl. Chem. 1983, 55, 1273-1280.
    • Furanosyl ring puckers are indicated with n-endo and n-exo designations, where all ring atoms except n are in the same plane. Atom n is displaced toward the 5′-substituent in n-endo conformers and away in n-exo. (a) Joint Commission on Biochemical Nomenclature. Pure Appl. Chem. 1983, 55, 1273-1280.
  • 89
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    • 14C KIE of 1.013-1.017, outside the error range of the experimental value.
    • 14C KIE of 1.013-1.017, outside the error range of the experimental value.
  • 95
    • 34250169897 scopus 로고    scopus 로고
    • 2O, not a combination of both. Noncompetitive KIEs reflect the rate-limiting step of a reaction, rather than the first irreversible step. A priori, the rate-limiting step in dAMP hydrolysis might be expected to be N7 protonation or C-N bond cleavage. The inverse solvent deuterium KIE demonstrates that it is the latter.
    • 2O, not a combination of both. Noncompetitive KIEs reflect the rate-limiting step of a reaction, rather than the first irreversible step. A priori, the rate-limiting step in dAMP hydrolysis might be expected to be N7 protonation or C-N bond cleavage. The inverse solvent deuterium KIE demonstrates that it is the latter.
  • 104
    • 34250219726 scopus 로고    scopus 로고
    • 1 is the bond length for a single bond between atoms of elements i and j. Single bond lengths were C-C, 1.526 Å; C-N, 1.475 Å; C-O, 1.41 Å; and C-H, 1.09 Å. (a) Johnston, H. S. Gas Phase Reaction Rate Theory; Ronald Press, Co.; New York, 1966.
    • 1 is the bond length for a single bond between atoms of elements i and j. Single bond lengths were C-C, 1.526 Å; C-N, 1.475 Å; C-O, 1.41 Å; and C-H, 1.09 Å. (a) Johnston, H. S. Gas Phase Reaction Rate Theory; Ronald Press, Co.; New York, 1966.


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