A New Approach to Possible Substrate Binding Mechanisms for Nitrile Hydratase.
From: Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa. ozlem@tuks.co.za
Biochemical and biophysical research communications
- Publish Date: Apr 2006
- ISSN: 0006-291X
- Volume: 343
- Issue: 1
- Pages: 319-25
- Medium: Print
- Language: English
- Citation (JAMA): Taştan Bishop A Ozlem, Sewell Trevor, et al. A New Approach to Possible Substrate Binding Mechanisms for Nitrile Hydratase.. Biochem. Biophys. Res. Commun. Apr 2006;343:319-25
Abstract
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.
Mesh Headings (Keywords): Actinomycetales, Bacterial Proteins, Binding Sites, Hydro-Lyases, Protein Conformation, Substrate Specificity
Check for Full Text / PubMed Unique Identifier (PMID): 16540090
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