1Y6H

Crystal structure of LIPDF

「1RN5」から置き換えられました

1Y6H の概要

• エントリーDOI: 10.2210/pdb1y6h/pdb
• 分子名称: Peptide deformylase, ZINC ION, FORMIC ACID, ... (5 entities in total)
• 機能のキーワード: open and close conformation, pdf, hydrolase
• 由来する生物種: Leptospira interrogans
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 41122.32

構造登録者

Zhou, Z.,Song, X.,Li, Y.,Gong, W. (登録日: 2004-12-06, 公開日: 2004-12-21, 最終更新日: 2024-03-13)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.2 Å)