The carboxylate shift in zinc enzymes: a computational study.
Zinc is the second most abundant transition element in biology and the only metal known to be represented in enzymes from each one of the six classes established by the International Union of Biochemistry. The flexible coordination geometry, the fast ligand exchange, the lack of redox activity, and its role as Lewis acid are just some of the features that make zinc an invaluable element in biological catalysis. In this study, we have analyzed the importance in mononuclear Zn enzymes of an interesting mechanistic phenomenon known as carboxylate shift, which is characterized by a change in the coordination mode of a carboxylate group (mono to bidentate or vice versa) with both ligand entrance or exit from the metal coordination sphere. Using B3LYP calculations, we were able to unveil in detail patterns relating the intrinsic characteristics of a given Zn coordination sphere with the existence or not of a carboxylate-shift mechanism and the additional energy stabilization arising from it. In particular, a specific Zn coordination sphere containing a carboxylate ligand (Asp or Glu), a cysteine, and a histidine has been shown to have the most favorable combination of amino acid residues that ensures a fast ligand exchange.
Sousa
Sérgio F
SF
REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
Fernandes
Pedro A
PA
Ramos
Maria João
MJ
D001224:Aspartic Acid / Q000737:chemistry; D002264:Carboxylic Acids / Q000737:chemistry*; D020134:Catalytic Domain; D019295:Computational Biology; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry; D004579:Electron Transport; D004798:Enzymes / Q000737:chemistry*; D018698:Glutamic Acid / Q000737:chemistry; D006639:Histidine / Q000737:chemistry; D008024:Ligands; D008667:Metalloproteins / Q000737:chemistry*; D010100:Oxygen / Q000737:chemistry; D011487:Protein Conformation; D015032:Zinc / Q000737:chemistry*
D002264:Carboxylic Acids; D004798:Enzymes; D008024:Ligands; D008667:Metalloproteins; D001224:Aspartic Acid; D018698:Glutamic Acid; D006639:Histidine; D015032:Zinc; D003545:Cysteine; D010100:Oxygen