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PDBsum entry 3fid
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Membrane protein
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PDB id
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3fid
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References listed in PDB file
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Key reference
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Title
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Active-Site architecture and catalytic mechanism of the lipid a deacylase lpxr of salmonella typhimurium.
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Authors
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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.
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Ref.
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Proc Natl Acad Sci U S A, 2009,
106,
1960-1964.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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