Farnesyltransferase--new insights into the zinc-coordination sphere paradigm: evidence for a carboxylate-shift mechanism.
Despite the enormous interest that has been devoted to the study of farnesyltransferase, many questions concerning its catalytic mechanism remain unanswered. In particular, several doubts exist on the structure of the active-site zinc coordination sphere, more precisely on the nature of the fourth ligand, which is displaced during the catalytic reaction by a peptide thiolate. From available crystallographic structures, and mainly from x-ray absorption fine structure data, two possible alternatives emerge: a tightly zinc-bound water molecule or an almost symmetrical bidentate aspartate residue (Asp-297beta). In this study, high-level theoretical calculations, with different-sized active site models, were used to elucidate this aspect. Our results demonstrate that both coordination alternatives lie in a notably close energetic proximity, even though the bidentate hypothesis has a somewhat lower energy. The Gibbs reaction and activation energies for the mono-bidentate conversion, as well as the structure for the corresponding transition state, were also determined. Globally, these results indicate that at room temperature the mono-bidentate conversion is reversible and very fast, and that probably both states exist in equilibrium, which suggests that a carboxylate-shift mechanism may have a key role in the farnesylation process by assisting the coordination/displacement of ligands to the zinc ion, thereby controlling the enzyme activity. Based on this equilibrium hypothesis, an explanation for the existing contradictions between the crystallographic and x-ray absorption fine structure results is proposed.
Sousa
Sérgio F
SF
REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
Fernandes
Pedro A
PA
Ramos
Maria João
MJ
D019883:Alkyl and Aryl Transferases / Q000737:chemistry*; D016880:Anisotropy; D001224:Aspartic Acid / Q000737:chemistry; D001665:Binding Sites; D001703:Biophysics / Q000379:methods; D002264:Carboxylic Acids / Q000737:chemistry; D002384:Catalysis; D018360:Crystallography, X-Ray; D051231:Farnesyltranstransferase; D007477:Ions; D008024:Ligands; D008958:Models, Molecular; D016011:Normal Distribution; D010100:Oxygen / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017368:Protein Prenylation; D017433:Protein Structure, Secondary; D013053:Spectrophotometry; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry; D014965:X-Rays; D015032:Zinc / Q000737:chemistry*
D002264:Carboxylic Acids; D007477:Ions; D008024:Ligands; D010455:Peptides; D014867:Water; D001224:Aspartic Acid; D019883:Alkyl and Aryl Transferases; D051231:Farnesyltranstransferase; D015032:Zinc; D010100:Oxygen