Ureases: quantum chemical calculations on cluster models.
Herein, we present results from a computational study of dinickel complexes that are relevant to the catalytic hydrolysis of urea exerted by the urease enzymes. The B3LYP density functional is used to characterize the equilibrium geometry, electronic and magnetic properties, and energies for a series of realistic complexes modeling the active site of ureases. The analysis of the theoretical results gives new insight into the structure, substrate binding, and catalytic mechanism. The water bridge between the two Ni(II) ions observed in the crystallographic structures of the ureases was assigned to a hydroxide bridge in agreement with the observed small antiferromagnetic coupling. Both monodentate and bidentate urea-bound complexes, in which urea had favorable orientations for catalysis, were characterized. Finally, two reaction mechanisms were investigated starting from the monodentate and bidentate urea-bound complexes, respectively. Both a Ni1...Ni2 bridging hydroxide and a Ni2-bound water molecule play crucial roles in the two mechanisms.
Suárez
Dimas
D
Departamento de Química Física y Analítica, Universidad de Oviedo, C/ Julián Clavería 8, 33006 Oviedo, Asturias, Spain.
Díaz
Natalia
N
Merz
Kenneth M
KM
D001407:Bacillus / Q000201:enzymology; D001665:Binding Sites; D018360:Crystallography, X-Ray; D021902:Enterobacter aerogenes / Q000201:enzymology; D006868:Hydrolysis; D006878:Hydroxides / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009532:Nickel / Q000737:chemistry / Q000378:metabolism; D011789:Quantum Theory; D013816:Thermodynamics; D014508:Urea / Q000737:chemistry / Q000378:metabolism; D014510:Urease / Q000737:chemistry* / Q000378:metabolism*
D006878:Hydroxides; D009532:Nickel; D014508:Urea; D014510:Urease