Theoretical investigation of the hydride transfer from formate to NAD+ and the implications for the catalytic mechanism of formate dehydrogenase

被引:33
作者
Schiott, B [1 ]
Zheng, YJ [1 ]
Bruice, TC [1 ]
机构
[1] Univ Calif Santa Barbara, Dept Chem, Santa Barbara, CA 93106 USA
关键词
D O I
10.1021/ja9807338
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The hydride transfer reaction between formate and NAD(+) has been investigated by using molecular orbital theory in combination with continuum solvation models. The reaction in the gas phase is extremely exothermic due to the instability of the charged reactant species. The calculations reveal that during the hydride transfer the pyridine ring of NAD(+) takes a quasi-boat conformation. The nitrogen atom of the pyridine ring remains planar, which is in agreement with the experimentally established N-15 kinetic isotope effect (1.004 +/- 0.001) of the formate dehydrogenase catalyzed oxidation of formate to carbon dioxide. The computed value at the HF/6-31+G(d,p) level of theory for the N-15 kinetic isotope effect is 1.0042. In solution, however, there is a potential energy barrier for the hydride transfer. At the MP2/6-31G(d)//HF/6-31G(d) level of theory the self-consistent reaction field approach gives a barrier height of 9.0 kcal/mol in acetonitrile (epsilon = 35.9). Direct nucleophilic addition of one of the carboxylate oxygens of formate to the pyridine ring of NAD(+) competes with hydride transfer, and this study reveals that this nucleophilic addition is likely to be preferred over the hydride transfer in the gas phase. Thus, the NAD(+)-dependent formate dehydrogenase must orient the substrate formate in the active site in such a fashion as to prevent this competing reaction from occurring. According to the recently solved X-ray crystal structure, it is clear that the Arg-284 and Asn-146 are the two critical amino acid residues that hold formate in the productive orientation for hydride transfer.
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页码:7192 / 7200
页数:9
相关论文
共 58 条
[11]  
Buck HM, 1996, RECL TRAV CHIM PAY B, V115, P329
[12]   SECONDARY DEUTERIUM AND N-15 ISOTOPE EFFECTS IN ENZYME-CATALYZED REACTIONS - CHEMICAL MECHANISM OF LIVER ALCOHOL-DEHYDROGENASE [J].
COOK, PF ;
OPPENHEIMER, NJ ;
CLELAND, WW .
BIOCHEMISTRY, 1981, 20 (07) :1817-1825
[13]   AM1-SM2 AND PM3-SM3 PARAMETERIZED SCF SOLVATION MODELS FOR FREE-ENERGIES IN AQUEOUS-SOLUTION [J].
CRAMER, CJ ;
TRUHLAR, DG .
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1992, 6 (06) :629-666
[14]   MECHANISTIC ASPECTS OF BIOLOGICAL REDOX REACTIONS INVOLVING NADH .2. A COMBINED SEMIEMPIRICAL AND ABINITIO STUDY OF HYDRIDE-ION TRANSFER BETWEEN THE NADH ANALOG, 1-METHYL-DIHYDRONICOTINAMIDE, AND FOLATE AND DIHYDROFOLATE ANALOG SUBSTRATES OF DIHYDROFOLATE-REDUCTASE [J].
CUMMINS, PL ;
GREADY, JE .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1990, 11 (07) :791-804
[15]   Simulation of the enzyme reaction mechanism of malate dehydrogenase [J].
Cunningham, MA ;
Ho, LL ;
Nguyen, DT ;
Gillilan, RE ;
Bash, PA .
BIOCHEMISTRY, 1997, 36 (16) :4800-4816
[16]   THE DEVELOPMENT AND USE OF QUANTUM-MECHANICAL MOLECULAR-MODELS .76. AM1 - A NEW GENERAL-PURPOSE QUANTUM-MECHANICAL MOLECULAR-MODEL [J].
DEWAR, MJS ;
ZOEBISCH, EG ;
HEALY, EF ;
STEWART, JJP .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1985, 107 (13) :3902-3909
[17]  
Frisch M.J., 1995, GAUSSIAN 94 REVISION
[18]  
GANDOUR RD, 1978, TRANSITION STATES BI
[19]   Kinetic isotope effects and transition state geometries. A theoretical investigation of E2 model systems [J].
Glad, SS ;
Jensen, F .
JOURNAL OF ORGANIC CHEMISTRY, 1997, 62 (02) :253-260
[20]   REACTION-PATH FOLLOWING IN MASS-WEIGHTED INTERNAL COORDINATES [J].
GONZALEZ, C ;
SCHLEGEL, HB .
JOURNAL OF PHYSICAL CHEMISTRY, 1990, 94 (14) :5523-5527