1y6h

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Revision as of 04:28, 21 November 2007

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spinqualitylabelsall models 1y6h, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Crystal structure of LIPDF

Overview

Peptide deformylase (PDF), which is essential for normal growth of, bacteria but not for higher organisms, is explored as an attractive target, for developing novel antibiotics. Here, we present the crystal structure, of Leptospira interrogans PDF (LiPDF) at 2.2A resolution. To our, knowledge, this is the first crystal structure of PDF associating in a, stable dimer. The key loop (named the CD-loop: amino acid residues 66-76), near the active-site pocket adopts "closed" or "open" conformations in the, two monomers forming the dimer. In the closed subunit, the CD-loop and, residue Arg109 block the entry of the substrate-binding pocket, while the, active-site pocket of the open subunit is occupied by the C-terminal tail, from the neighbouring molecule. Moreover, a formate group, as one product, of deformylisation, is observed bound with the active-site zinc ion. LiPDF, displays significant structural differences in the C-terminal region, compared to both type-I and type-II PDFs, suggesting a new family of PDFs.

About this Structure

1Y6H is a Single protein structure of sequence from Leptospira interrogans with ZN, GLY and FMT as ligands. This structure superseeds the now removed PDB entry 1RN5. Active as Peptide deformylase, with EC number 3.5.1.88 Full crystallographic information is available from OCA.

Reference

Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans., Zhou Z, Song X, Li Y, Gong W, J Mol Biol. 2004 May 21;339(1):207-15. PMID:15123432

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