1Y6H

Crystal structure of LIPDF

Replaces:  1RN5

Summary for 1Y6H

• Entry DOI: 10.2210/pdb1y6h/pdb
• Descriptor: Peptide deformylase, ZINC ION, FORMIC ACID, ... (5 entities in total)
• Functional Keywords: open and close conformation, pdf, hydrolase
• Biological source: Leptospira interrogans
• Total number of polymer chains: 2
• Total formula weight: 41122.32

Authors

Zhou, Z.,Song, X.,Li, Y.,Gong, W. (deposition date: 2004-12-06, release date: 2004-12-21, Last modification date: 2024-03-13)

Primary citation

Zhou, Z.,Song, X.,Li, Y.,Gong, W.
Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans
J.Mol.Biol., 339:207-215, 2004

PubMed Abstract: 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.

PubMed: 15123432
DOI: 10.1016/j.jmb.2004.03.045

Experimental method

X-RAY DIFFRACTION (2.2 Å)