Open AccessInvestigation of zinc‐containing peptide deformylase from Leptospira interrogans by X‐ray absorption near‐edge spectroscopy
Author(s) -
Li Shujun,
Zhou Zhaocai,
Chu Wangsheng,
Gong Weimin,
Benfatto Maurizio,
Hu Tiandou,
Xie Yaning,
Xian Dingchang,
Wu Ziyu
Publication year - 2005
Publication title -
journal of synchrotron radiation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.172
H-Index - 99
ISSN - 1600-5775
DOI - 10.1107/s0909049504031413
Subject(s) - xanes , zinc , chemistry , crystallography , absorption (acoustics) , metal , ion , spectroscopy , molecule , absorption spectroscopy , x ray absorption fine structure , metal ions in aqueous solution , x ray absorption spectroscopy , materials science , organic chemistry , optics , physics , quantum mechanics , composite material
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.