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PDBsum entry 2vpy
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Oxidoreductase
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PDB id
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2vpy
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Contents |
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735 a.a.
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194 a.a.
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251 a.a.
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References listed in PDB file
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Key reference
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Title
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Molecular mechanism of energy conservation in polysulfide respiration.
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Authors
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M.Jormakka,
K.Yokoyama,
T.Yano,
M.Tamakoshi,
S.Akimoto,
T.Shimamura,
P.Curmi,
S.Iwata.
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Ref.
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Nat Struct Biol, 2008,
15,
730-737.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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Bacterial polysulfide reductase (PsrABC) is an integral membrane protein complex
responsible for quinone-coupled reduction of polysulfide, a process important in
extreme environments such as deep-sea vents and hot springs. We determined the
structure of polysulfide reductase from Thermus thermophilus at 2.4-A
resolution, revealing how the PsrA subunit recognizes and reduces its unique
polyanionic substrate. The integral membrane subunit PsrC was characterized
using the natural substrate menaquinone-7 and inhibitors, providing a
comprehensive representation of a quinone binding site and revealing the
presence of a water-filled cavity connecting the quinone binding site on the
periplasmic side to the cytoplasm. These results suggest that polysulfide
reductase could be a key energy-conserving enzyme of the T. thermophilus
respiratory chain, using polysulfide as the terminal electron acceptor and
pumping protons across the membrane via a previously unknown mechanism.
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Figure 1.
Ribbon representation of the PsrABC dimer viewed parallel to
the membrane, with one monomer shown in light gray for clarity.
The PsrA, PsrB and PsrC subunits in the monomer to the left are
green, ruby and blue, respectively. The MGD cofactors are orange
with molybdenum shown as a black sphere. Five [4Fe-4S] clusters
are shown in red (iron atoms) and yellow (sulfur atoms), and PCP
is shown in black. All distances, including edge-to-edge
distances between redox centres, are in given in angstroms. In
the catalytic cycle of Psr, menaquinol is reduced on the
periplasmic side of the membrane, releasing two protons and
electrons (dotted line). The electrons are transported via the
iron-sulfur clusters to the active-site molybdenum, where
polysulfide is reduced with the evolution of hydrogen sulfide.
All structural figures were made using PyMol
(http://pymol.sourceforge.net/).
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Figure 2.
(a) 2F[o] – F[c] electron density map (blue) is shown for
ArgA332 and w201, and F[o] – F[c] map (red) is shown at the
position for the oxo (=O) group (omit map for the oxo) bound to
the molydenum atom. Maps are contoured at 2  and
4 ,
respectively. Hydrogen bonds between ArgA332 and water molecules
are shown as dotted lines. (b) Stereoviews of the active site
and putative proton-delivery channel in PsrA. The surface and
interior of the protein are shown in light and dark gray,
respectively. Crystallographic water molecules are shown as red
spheres.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2008,
15,
730-737)
copyright 2008.
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