Computational studies on nonenzymatic and enzymatic pyridoxal phosphate catalyzed decarboxylations of 2-aminoisobutyrate.
A computational study of nonenzymatic and enzymatic pyridoxal phosphate-catalyzed decarboxylation of 2-aminoisobutyrate (AIB) is presented. Four prototropic isomers of a model aldimine between AIB and 5'-deoxypyridoxal, with acetate interacting with the pyridine nitrogen, were employed in calculations of both gas phase and water model (PM3 and PM3-SM3) decarboxylation reaction paths. Calculations employing the transition state structures obtained for the four isomers allow the demonstration of stereoelectronic effects in transition state stabilization as well as a separation of the contributions of the Schiff base and pyridine ring moieties to this stabilization. The unprotonated Schiff base contribution (approximately 16 kcal/mol) is larger than that of the pyridine ring even when it is protonated (approximately 10 kcal/mol), providing an explanation of the catalytic power of pyruvoyl-dependent amino acid decarboxylases. An active site model of dialkylglycine decarboxylase was constructed and validated, and enzymatic decarboxylation reaction paths were calculated. The reaction coordinate is shown to be complex, with proton transfer from Lys272 to the coenzyme C4' likely simultaneous with C alpha--CO(2)(-) bond cleavage. The proposed concerted decarboxylation/proton-transfer mechanism provides a simple explanation for the observed specificity of this enzyme toward oxidative decarboxylation.
Toney
M D
MD
Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA. toney@chem.ucdavis.edu
D000621:Aminoisobutyric Acids / Q000737:chemistry*; D001665:Binding Sites; D002262:Carboxy-Lyases / Q000737:chemistry*; D002384:Catalysis; D003198:Computer Simulation; D003653:Decarboxylation; D004734:Energy Metabolism; D007097:Imines / Q000737:chemistry; D008432:Mathematical Computing; D008956:Models, Chemical; D008958:Models, Molecular; D011725:Pyridines / Q000737:chemistry; D011732:Pyridoxal Phosphate / Q000737:chemistry*; D012545:Schiff Bases / Q000737:chemistry; D012984:Software; D013237:Stereoisomerism; D013816:Thermodynamics
D000621:Aminoisobutyric Acids; D007097:Imines; D011725:Pyridines; D012545:Schiff Bases; C100049:2-aminoisobutyric acid; D011732:Pyridoxal Phosphate; D002262:Carboxy-Lyases; C063519:2,2-dialkylglycine decarboxylase; C023666:pyridine