Molecular modeling of the complexes between Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase and the ATP analogs pyridoxal 5 '-diphosphoadenosine and pyridoxal 5 '-triphosphoadenosine. Specific labeling of lysine 290

Molecular mechanics calculations have been employed to obtain models of the complexes between Saccharomyces cerevisiae phosphoenolpyruvate (PEP) kinas e and the ATP analogs pyridoxal 5'-diphosphoadenosine (PLP-AMP) and pyridox al 5'-triphosphoadenosine (PLP-ADP), using the crystalline coordinates of t he ATP-pyruvate-Mn2+-Mg2+ complex of Escherichia coli PEP carboxykinase [Ta ri et al. (1997), Nature Struct. Biol. 4, 990-994]. In these models, the pr eferred conformation of the pyridoxyl moiety of PLP-ADP and PLP-AMP was est ablished through rotational barrier and simulated annealing procedures. Dis tances from the carbonyl-C of each analog to epsilon-N of active-site lysyl residues were calculated for the most stable enzyme-analog complex conform ation, and it was found that the closest epsilon-N is that from Lys(290), t hus predicting Schiff base formation between the corresponding carbonyl and amino groups. This prediction was experimentally verified through chemical modification of S. cerevisiae PEP carboxykinase with PLP-ADP and PLP-AMP. The results here described demonstrate the use of molecular modeling proced ures when planning chemical modification of enzyme-active sites.