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- Title
How water molecules affect the catalytic activity of hydrolases - A XANES study of the local structures of peptide deformylase.
- Authors
Peixin Cui; Yu Wang; Wangsheng Chu; Xiaoyun Guo; Feifei Yang; Meijuan Yu; Haifeng Zhao; Yuhui Dong; Yaning Xie; Weimin Gong; Ziyu Wu
- Abstract
Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pHvalues and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55Å.
- Subjects
PEPTIDE deformylase; MOLECULAR structure of water; HYDROLASE kinetics; X-ray absorption near edge structure; PROKARYOTES; PROTEIN synthesis; AB initio quantum chemistry methods; METAL ions
- Publication
Scientific Reports, 2014, p1
- ISSN
2045-2322
- Publication type
Article
- DOI
10.1038/srep07453