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PDBsum entry 1vgo
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Proton transport
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PDB id
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1vgo
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References listed in PDB file
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Key reference
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Title
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Crystal structures of archaerhodopsin-1 and -2: common structural motif in archaeal light-Driven proton pumps.
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Authors
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N.Enami,
K.Yoshimura,
M.Murakami,
H.Okumura,
K.Ihara,
T.Kouyama.
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Ref.
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J Mol Biol, 2006,
358,
675-685.
[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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Archaerhodopsin-1 and -2 (aR-1 and aR-2) are light-driven proton pumps found in
Halorubrum sp. aus-1 and -2, which share 55-58% sequence identity with
bacteriorhodopsin (bR), a proton pump found in Halobacterium salinarum. In this
study, aR-1 and aR-2 were crystallized into 3D crystals belonging to P4(3)2(1)2
(a = b = 128.1 A, c = 117.6 A) and C222(1) (a = 122.9 A, b = 139.5 A, c = 108.1
A), respectively. In both the crystals, the asymmetric unit contains two protein
molecules with slightly different conformations. Each subunit is composed of
seven helical segments as seen in bR but, unlike bR, aR-1 as well as aR-2 has a
unique omega loop near the N terminus. It is found that the proton pathway in
the extracellular half (i.e. the proton release channel) is more opened in aR-2
than in aR-1 or bR. This structural difference accounts for a large variation in
the pKa of the acid purple-to-blue transition among the three proton pumps. All
the aromatic residues surrounding the retinal polyene chain are conserved among
the three proton pumps, confirming a previous argument that these residues are
required for the stereo-specificity of the retinal isomerization. In the
cytoplasmic half, the region surrounded by helices B, C and G is highly
conserved, while the structural conservation is very low for residues extruded
from helices E and F. Structural conservation of the hydrophobic residues
located on the proton uptake pathway suggests that their precise arrangement is
necessary to prevent a backward flow of proton in the presence of a large pH
gradient and membrane potential. An empty cavity is commonly seen in the
vicinity of Leu93 contacting the retinal C13 methyl. Existence of such a cavity
is required to allow a large rotation of the side-chain of Leu93 at the early
stage of the photocycle, which has been shown to accompany water translocation
across the Schiff base.
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Figure 6.
Figure 6. Structural comparison of the cytoplasmic halves of
aR-1, aR-2 and bR. Carbon atoms in aR-2 (subunit-I),
aR-1(subunit-I) and bR are drawn in gold, yellow and cyan,
respectively, and nitrogen and oxygen atoms in all the proteins
are in blue and red, respectively.
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Figure 7.
Figure 7. Micro-cavities in the light-adapted states of aR-2
(a), aR-1 (b) and bR (c) and in the L intermediate of bR (d). In
(a) and (b), two subunits contained in the asymmetric unit are
superimposed and micro-cavities in the subunits I and II are
drawn in yellow and cyan, respectively; the micro-cavities
observed commonly in both the subunits are in green. In (c) and
(d), micro-cavities are drawn in cyan. Some important residues
(Arg82, Leu93, Asp96, Lys216 and retinal) are represented with a
ball-and-stick model. Red spheres in (a), (c) and (d) represent
water molecules. Since the proton release channel in aR-2 is so
opened that cavity VI is actually connected to the solvent
region, this cavity is visualized by placing an artificial
polypeptide near the outlet of the proton release channel. This
Figure was drawn with Swiss-PdbViewer.^48
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
358,
675-685)
copyright 2006.
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