1vev

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spinqualitylabelsall models 1vev, resolution 2.51Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Crystal structure of peptide deformylase from Leptospira Interrogans (LiPDF) at pH6.5

Overview

Peptide deformylase is an attractive target for developing novel, antibiotics. Previous studies at pH 3.0 showed peptide deformylase from, Leptospira interrogans (LiPDF) exists as a dimer in which one monomer is, in a closed form and the other is in an open form, with different, conformations of the CD-loop controlling the entrance to the active, pocket. Here we present structures of LiPDF at its active pH range. LiPDF, forms a similar dimer at pH values 6.5-8.0 as it does at pH 3.0., Interestingly, both of the monomers are almost in the same closed form as, that observed at pH 3.0. However, when the enzyme is complexed with the, natural inhibitor actinotin, the conformation of the CD-loop is half-open., Two pairs of Arg109-mediated cation-pi interactions, as well as hydrogen, bonds, have been identified to stabilize the different CD-loop, conformations. These results indicate that LiPDF may be found in different, structural states, a feature that has never before been observed in the, peptide deformylase family. Based on our results, a novel substrate, binding model, featured by an equilibrium between the closed and the open, forms, is proposed. Our results present crystallographic evidence, supporting population shift theory, which is distinguished from the, conventional lock-and-key or induced-fit models. These results not only, facilitate the development of peptide deformylase-targeted drugs but also, provide structural insights into the mechanism of an unusual type of, protein binding event.

About this Structure

1VEV is a Single protein structure of sequence from Leptospira interrogans with ZN, MES and FMT as ligands. Active as Peptide deformylase, with EC number 3.5.1.88 Full crystallographic information is available from OCA.

Reference

Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift., Zhou Z, Song X, Gong W, J Biol Chem. 2005 Dec 23;280(51):42391-6. Epub 2005 Oct 20. PMID:16239225

Page seeded by OCA on Wed Nov 21 04:47:23 2007