title: Investigation of zinc-containing peptide deformylase from Leptospira interrogans by X-ray absorption near-edge spectroscopy.
abstract: Peptide deformylase (PDF, EC 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. Recently, PDF has been studied as a target for new antibiotics. Its activity is strongly dependent on the bound metal ion. The crystallographic studies did not show any significant structural difference upon various bound metal ions. In this paper, X-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of PDF from Leptospira interrogans in dry powder. XANES (X-ray absorption near-edge structure) calculations were performed and the local geometry of the active center was reconstructed successfully. By comparing with the crystal structure of an enzyme-product complex, the results from calculations show that a water molecule has moved towards the zinc ion and lies in the distance range to coordinate with the zinc ion weakly.
authors.affiliation: Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 100039 Beijing, People's Republic of China.
authors.forename: Shujun
authors.initials: S
authors.lastname: Li
authors.forename: Zhaocai
authors.initials: Z
authors.lastname: Zhou
authors.forename: Wangsheng
authors.initials: W
authors.lastname: Chu
authors.forename: Weimin
authors.initials: W
authors.lastname: Gong
authors.forename: Maurizio
authors.initials: M
authors.lastname: Benfatto
authors.forename: Tiandou
authors.initials: T
authors.lastname: Hu
authors.forename: Yaning
authors.initials: Y
authors.lastname: Xie
authors.forename: Dingchang
authors.initials: D
authors.lastname: Xian
authors.forename: Ziyu
authors.initials: Z
authors.lastname: Wu
mesh_terms: D000581:Amidohydrolases / Q000737:chemistry*; D002384:Catalysis; D007921:Leptospira interrogans / Q000201:enzymology*; D015394:Molecular Structure; D013057:Spectrum Analysis / Q000379:methods*; D014965:X-Rays; D015032:Zinc / Q000737:chemistry*
chemical_list: D000581:Amidohydrolases; C084507:peptide deformylase; D015032:Zinc