title: 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.
abstract: Molecular mechanics calculations have been employed to obtain models of the complexes between Saccharomyces cerevisiae phosphoenolpyruvate (PEP) kinase and the ATP analogs pyridoxal 5'-diphosphoadenosine (PLP-AMP) and pyridoxal 5'-triphosphoadenosine (PLP-ADP), using the crystalline coordinates of the ATP-pyruvate-Mn(2+)-Mg(2+) complex of Escherichia coli PEP carboxykinase [Tari et al. (1997), Nature Struct. Biol. 4, 990-994]. In these models, the preferred conformation of the pyridoxyl moiety of PLP-ADP and PLP-AMP was established through rotational barrier and simulated annealing procedures. Distances from the carbonyl-C of each analog to epsilon-N of active-site lysyl residues were calculated for the most stable enzyme-analog complex conformation, and it was found that the closest epsilon-N is that from Lys(290), thus 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 procedures when planning chemical modification of enzyme-active sites.
authors.affiliation: Departamento de Ciencias Químicas, Facultad de Química y Biología, Universidad de Santiago de Chile.
authors.forename: F D
authors.initials: FD
authors.lastname: González-Nilo
authors.forename: R
authors.initials: R
authors.lastname: Vega
authors.forename: E
authors.initials: E
authors.lastname: Cardemil
mesh_terms: D000244:Adenosine Diphosphate / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism*; D000255:Adenosine Triphosphate / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D002851:Chromatography, High Pressure Liquid; D007700:Kinetics; D008958:Models, Molecular; D019764:Phosphoenolpyruvate Carboxykinase (ATP) / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D011732:Pyridoxal Phosphate / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000201:enzymology*
chemical_list: C417675:pyridoxal 5'-triphosphoadenosine; D011732:Pyridoxal Phosphate; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; D019764:Phosphoenolpyruvate Carboxykinase (ATP); C048236:pyridoxal 5'-diphospho-5'-adenosine