Theoretical studies on pyridoxal 5'-phosphate-dependent transamination of alpha-amino acids.
Density functional methods have been applied to investigate the irreversible transamination between glyoxylic acid and pyridoxamine analog and the catalytic mechanism for the critical [1,3] proton transfer step in aspartate aminotransferase (AATase). The results indicate that the catalytic effect of pyridoxal 5'-phosphate (PLP) may be attributed to its ability to stabilize related transition states through structural resonance. Additionally, the PLP hydroxyl group and the carboxylic group of the amino acid can shuttle proton, thereby lowering the barrier. The rate-limiting step is the tautomeric conversion of the aldimine to ketimine by [1,3] proton transfer, with a barrier of 36.3 kcal/mol in water solvent. A quantum chemical model consisting 142 atoms was constructed based on the crystal structure of the native AATase complex with the product L-glutamate. The electron-withdrawing stabilization by various residues, involving Arg386, Tyr225, Asp222, Asn194, and peptide backbone, enhances the carbon acidity of 4'-C of PLP and Calpha of amino acid. The calculations support the proposed proton transfer mechanism in which Lys258 acts as a base to shuttle a proton from the 4'-C of PLP to Calpha of amino acid. The first step (proton transfer from 4'-C to lysine) is shown to be the rate-limiting step. Furthermore, we provided an explanation for the reversibility and specificity of the transamination in AATase.
Liao
Rong-Zhen
RZ
College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China.
Ding
Wan-Jian
WJ
Yu
Jian-Guo
JG
Fang
Wei-Hai
WH
Liu
Ruo-Zhuang
RZ
D000586:Amination; D000596:Amino Acids / Q000378:metabolism*; D001219:Aspartate Aminotransferases / Q000378:metabolism; D018698:Glutamic Acid / Q000378:metabolism; D008962:Models, Theoretical; D011522:Protons; D011732:Pyridoxal Phosphate; D011789:Quantum Theory
D000596:Amino Acids; D011522:Protons; D018698:Glutamic Acid; D011732:Pyridoxal Phosphate; D001219:Aspartate Aminotransferases