PDBsum entry 3fid

Membrane protein

PDB id: 3fid

Contents

Protein chains

296 a.a. *

Ligands

GOL ×4

CXE ×8

Metals

_ZN ×9

Waters ×414

* Residue conservation analysis

PDB id:

3fid

Name:

Membrane protein

Title:

Lpxr from salmonella typhimurium

Structure:

Putative outer membrane protein (lpxr). Chain: a, b. Fragment: mature domain, unp residues 24-319. Engineered: yes

Source:

Salmonella typhimurium. Organism_taxid: 602. Strain: strain lt2. Gene: lpxr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.193 R-free: 0.230

Authors:

L.Rutten,P.Gros

Key ref:

L.Rutten et al. (2009). Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium. Proc Natl Acad Sci U S A, 106, 1960-1964. PubMed id: 19174515 DOI: 10.1073/pnas.0813064106

Date:

11-Dec-08 Release date: 10-Feb-09

Protein chains

Q8ZPT3  (Q8ZPT3_SALTY) -  Outer membrane protein from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 319 a.a.

Struc: 296 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0813064106

Proc Natl Acad Sci U S A 106:1960-1964 (2009)

PubMed id: 19174515

Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium.

L.Rutten, J.P.Mannie, C.M.Stead, C.R.Raetz, C.M.Reynolds, A.M.Bonvin, J.P.Tommassen, M.R.Egmond, M.S.Trent, P.Gros.

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.

Selected figure(s)

Figure 2.
Overall structure of LpxR. (A) Ribbon representation of LpxR. The ribbon is colored with a gradient from the N terminus in blue to the C terminus in red. Aromatic residues located at the membrane boundaries are shown as cyan sticks. Membrane boundaries are indicated by black lines. The extracellular side is located at the top of the figure, and the periplasmic side is at the bottom. Active-site residues are shown as yellow sticks. Zn^2+ atoms are shown as gray spheres, and glycerol molecules are shown as sticks in green. Loops, turns, the N terminus, and the C terminus are labeled. (B) LpxR viewed from the periplasmic side of the protein. The representation of the structure is similar to that in A. Figs. 2, 3, 4, S2, and S5 were prepared with PyMOL (23).

Figure 4.
Modeling of Kdo[2]–lipid A into the active site of LpxR and the proposed catalytic mechanism. (A) View of Kdo[2]–lipid A, which is shown in sticks with yellow carbons, modeled onto LpxR. Fully conserved residues are shown as sticks in cyan. Residues that are probably involved in binding of the Kdo sugars, i.e., K67, R68, and H25 are shown as blue sticks. D11 is shown in magenta. The calcium ion is shown as a gray sphere. (B) LpxR is shown as a surface representation in green with K67, R68, H25, D11, Kdo[2]–lipid A, and the calcium colored as in A. (C) Closeup of the catalytic site of the modeling result. The representation is the same as in A, with the exception that the view angle is different and that polar hydrogens are shown in white. (D) Proposed catalytic mechanism for LpxR. The substrate is shown in blue, protein residues are shown in cyan, the water and calcium are shown in black. The scissile bond is shown in red. Black arrows indicate the movement of the electron pairs.

Figures were selected by an automated process.