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PDBsum entry 1kb9
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Oxidoreductase/electron transport
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PDB id
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1kb9
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Contents |
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431 a.a.
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352 a.a.
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385 a.a.
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246 a.a.
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185 a.a.
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74 a.a.
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125 a.a.
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93 a.a.
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55 a.a.
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127 a.a.
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107 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Specific roles of protein-Phospholipid interactions in the yeast cytochrome bc1 complex structure.
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Authors
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C.Lange,
J.H.Nett,
B.L.Trumpower,
C.Hunte.
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Ref.
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EMBO J, 2001,
20,
6591-6600.
[DOI no: ]
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PubMed id
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Abstract
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Biochemical data have shown that specific, tightly bound phospholipids are
essential for activity of the cytochrome bc1 complex (QCR), an integral membrane
protein of the respiratory chain. However, the structure and function of such
phospholipids are not yet known. Here we describe five phospholipid molecules
and one detergent molecule in the X-ray structure of yeast QCR at 2.3 A
resolution. Their individual binding sites suggest specific roles in
facilitating structural and functional integrity of the enzyme. Interestingly, a
phosphatidylinositol molecule is bound in an unusual interhelical position near
the flexible linker region of the Rieske iron-sulfur protein. Two possible
proton uptake pathways at the ubiquinone reduction site have been identified:
the E/R and the CL/K pathway. Remarkably, cardiolipin is positioned at the
entrance to the latter. We propose that cardiolipin ensures structural integrity
of the proton-conducting protein environment and takes part directly in proton
uptake. Site-directed mutagenesis of ligating residues confirmed the importance
of the phosphatidylinositol- and cardiolipin-binding sites.
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Figure 5.
Figure 5 Section of the yeast QCR model showing L5
(cardiolipin), neighboring amino acid residues and water
molecules. Hydrogen bonds or ion pairs with the oxygen atoms of
the phosphodiester groups A and B of the cardiolipin headgroup
are indicated as dashed lines (Lys288, Lys289 of CYT1, Tyr28 of
COB). Water molecules are shown as balls, and other molecules in
stick presentation. The final 2F[o] - F[c] electron density map
(blue -gray) is contoured at 1.0  .
Atoms are shown in standard colors.
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Figure 7.
Figure 7 Putative proton uptake pathways at the Q[i] site of
yeast QCR via two arrays of hydrogen-bonded water molecules,
which connect the bulk solvent at the matrix side with the site
of ubiquinone reduction. The entrance to the E/R pathway is
formed by Glu52 of QCR7 and Wat176. The gating residue towards
the quinone-binding pocket is Arg218 of COB. Cardiolipin (L5) is
positioned at the entrance to the CL/K pathway, for which Lys228
of COB is the gating residue. Arrows indicate the access sites
from the bulk solvent, and double arrows show proton transfer
between the key residues Arg218 or Lys228 of COB and UQ6. Side
chains of amino acid residues that are involved in hydrogen bond
interactions or ion pair formation are shown (standard colors).
Dashed lines indicate hydrogen bond interactions. Dotted lines
are used for hydrogen bond interactions of UQ6 and CL ligands
(His202, Asp229 and Tyr28 of COB, and Lys288 and Lys289 of
CYT1). Water molecules in the cavity above the cardiolipin
headgroup are stabilized by interactions with side chains of
Lys228 of COB, Lys296 of CYT1 and His85 of QCR7. A surrounding
layer of non-polar residues (not shown) encloses the
water-filled cavity. Transmembrane helices are shown as ribbon
presentation and other polypeptide backbones as rope
presentation. UQ6, heme b[H] and CL are represented as stick
models.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2001,
20,
6591-6600)
copyright 2001.
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Secondary reference #1
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Title
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Structure at 2.3 a resolution of the cytochrome bc(1) complex from the yeast saccharomyces cerevisiae co-Crystallized with an antibody fv fragment.
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Authors
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C.Hunte,
J.Koepke,
C.Lange,
T.Rossmanith,
H.Michel.
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Ref.
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Structure, 2000,
8,
669-684.
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PubMed id
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