title: How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase.
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 pH values 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 2.55 Å.
authors.affiliation: 1] National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China [2] Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Peixin
authors.initials: P
authors.lastname: Cui
authors.affiliation: Shanghai Synchrotron Radiation Facilities, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: 1] National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China [2] Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Wangsheng
authors.initials: W
authors.lastname: Chu
authors.affiliation: 1] Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China [2] Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Xiaoyun
authors.initials: X
authors.lastname: Guo
authors.affiliation: National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.
authors.forename: Feifei
authors.initials: F
authors.lastname: Yang
authors.affiliation: Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Meijuan
authors.initials: M
authors.lastname: Yu
authors.affiliation: Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yuhui
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yaning
authors.initials: Y
authors.lastname: Xie
authors.affiliation: 1] Institute of Biophysics, Chinese Academy of Sciences, Beijing, China [2] Hefei National Laboratory for Physical Sciences at the microscale, University of Science and Technology of China.
authors.forename: Weimin
authors.initials: W
authors.lastname: Gong
authors.affiliation: 1] National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China [2] Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Ziyu
authors.initials: Z
authors.lastname: Wu
mesh_terms: D000581:Amidohydrolases / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D055162:Biocatalysis; D020134:Catalytic Domain; D056831:Coordination Complexes / Q000737:chemistry; D007919:Leptospira / Q000201:enzymology; D008958:Models, Molecular; D014867:Water / Q000737:chemistry*; D056928:X-Ray Absorption Spectroscopy; D015032:Zinc / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D056831:Coordination Complexes; D014867:Water; D000581:Amidohydrolases; C084507:peptide deformylase; D015032:Zinc