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PDBsum entry 1m0m
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Ion transport
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PDB id
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1m0m
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Contents |
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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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Crystallographic structure of the retinal and the protein after deprotonation of the schiff base: the switch in the bacteriorhodopsin photocycle.
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Authors
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J.Lanyi,
B.Schobert.
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Ref.
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J Mol Biol, 2002,
321,
727-737.
[DOI no: ]
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PubMed id
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Abstract
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We illuminated bacteriorhodopsin crystals at 210K to produce, in a
photostationary state with 60% occupancy, the earliest M intermediate (M1) of
the photocycle. The crystal structure of this state was then determined from
X-ray diffraction to 1.43 A resolution. When the refined model is placed after
the recently determined structure for the K intermediate but before the reported
structures for two later M states, a sequence of structural changes becomes
evident in which movements of protein atoms and bound water are coordinated with
relaxation of the initially strained photoisomerized 13-cis,15-anti retinal. In
the K state only retinal atoms are displaced, but in M1 water 402 moves also,
nearly 1A away from the unprotonated retinal Schiff base nitrogen. This breaks
the hydrogen bond that bridges them, and initiates rearrangements of the
hydrogen-bonded network of the extracellular region that develop more fully in
the intermediates that follow. In the M1 to M2 transition, relaxation of the
C14-C15 and C15=NZ torsion angles to near 180 degrees reorients the retinylidene
nitrogen atom from the extracellular to the cytoplasmic direction, water 402
becomes undetectable, and the side-chain of Arg82 is displaced strongly toward
Glu194 and Glu204. Finally, in the M2 to M2' transition, correlated with release
of a proton to the extracellular surface, the retinal assumes a virtually fully
relaxed bent shape, and the 13-methyl group thrusts against the indole ring of
Trp182 which tilts in the cytoplasmic direction. Comparison of the structures of
M1 and M2 reveals the principal switch in the photocycle: the change of the
angle of the C15=NZ-CE plane breaks the connection of the unprotonated Schiff
base to the extracellular side and establishes its connection to the cytoplasmic
side.
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Figure 2.
Figure 2. The 2F[obs] -F[calc] electron density maps at the
retinal Schiff base for (a) an illuminated crystal and (b) a
non-illuminated crystal. In both cases, refinement assumed two
conformations, at occupancies of 40% (unconverted BR state,
green) and 60% (M[1] state, grey), respectively, as discussed in
the text. Some atom notations in the retinal are given in (b).
The Figure was prepared with graphics program Setor.[60]
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Figure 3.
Figure 3. The 2F[obs] -F[calc] electron density maps at the
retinal, Asp85, Asp212 and water 402 for (a) an illuminated
crystal and (b) a non-illuminated crystal. As in Figure 2, the
two conformations, for the BR and M[1] states are indicated with
green and gray colors. The retinal Schiff base is labeled as NZ.
In (a) the hydrogen-bonds (in blue) are for the M[1] state, in
(b) they are (in yellow) for the BR state. The Figure was
prepared with the graphics program Setor.[60]
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2002,
321,
727-737)
copyright 2002.
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