3FID

LpxR from Salmonella typhimurium

3FID の概要

• エントリーDOI: 10.2210/pdb3fid/pdb
• 分子名称: Putative outer membrane protein (LpxR), ZINC ION, GLYCEROL, ... (5 entities in total)
• 機能のキーワード: lipopolysaccharide-modifying outer membrane enzyme, membrane protein
• 由来する生物種: Salmonella typhimurium
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 68825.38

構造登録者

Rutten, L.,Gros, P. (登録日: 2008-12-11, 公開日: 2009-02-10, 最終更新日: 2024-03-20)

主引用文献

Rutten, L.,Mannie, J.-P.B.A.,Stead, C.M.,Raetz, C.R.H.,Reynolds, C.M.,Bonvin, A.M.J.J.,Tommassen, J.P.,Egmond, M.R.,Trent, M.S.,Gros, P.
Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium
Proc.Natl.Acad.Sci.USA, 106:1960-1964, 2009

PubMed Abstract: The lipid A portion of lipopolysaccharide, the major component of the outer leaflet of the outer membrane of gram-negative bacteria, is toxic to humans. Modification of lipid A by enzymes often reduces its toxicity. The outer-membrane protein LpxR from Salmonella typhimurium is a lipid A-modifying enzyme. It removes the 3'-acyloxyacyl moiety of the lipid A portion of lipopolysaccharide in a Ca(2+)-dependent manner. Here, we present the crystal structure of S. typhimurium LpxR, crystallized in the presence of zinc ions. The structure, a 12-stranded beta-barrel, reveals that the active site is located between the barrel wall and an alpha-helix formed by an extracellular loop. Based on site-directed mutagenesis and modeling of a substrate on the active site, we propose a catalytic mechanism similar to that of phospholipase A2, in which a Ca(2+) forms the oxyanion hole and a histidine activates a water molecule (or a cascade of two water molecules) that subsequently attacks the carbonyl oxygen of the scissile bond.

PubMed: 19174515
DOI: 10.1073/pnas.0813064106

実験手法

X-RAY DIFFRACTION (1.9 Å)