A new approach to possible substrate binding mechanisms for nitrile hydratase.
We combined normal mode analysis (NMA) with cavity calculations as a method to get more insight into static crystal structures. We used nitrile hydratase (NHase) as a case study, and the crystal structure of a complex of Pseudonocardia thermophila NHase (1UGP) with n-butyric acid was chosen as a reference structure. The reference structure was compared with the other available NHase crystal structures. Cavity calculations of the static structures showed the entrances to the active site and also a possible function of the N-terminal in the substrate selection of the Co-type NHase. When NMA was combined with cavity calculations, a closing-opening passage was observed. Analysis of low frequency modes combined with cavity calculations led us to propose "breathing" and "flip-flop" mechanisms which might be a key part of the substrate binding mechanism.
Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa. ozlem@tuks.co.za
A Ozlem
AO
Taştan Bishop
Trevor
T
Sewell
D000192:Actinomycetales / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D006836:Hydro-Lyases / Q000737:chemistry*; D011487:Protein Conformation; D013379:Substrate Specificity
D001426:Bacterial Proteins; D006836:Hydro-Lyases; C048831:nitrile hydratase