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PDBsum entry 1c8s
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Ion transport
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PDB id
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1c8s
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Contents |
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* Residue conservation analysis
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DOI no:
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Science
286:255-261
(1999)
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PubMed id:
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Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution.
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H.Luecke,
B.Schobert,
H.T.Richter,
J.P.Cartailler,
J.K.Lanyi.
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ABSTRACT
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Crystal structures of the Asp96 to Asn mutant of the light-driven proton pump
bacteriorhodopsin and its M photointermediate produced by illumination at
ambient temperature have been determined to 1.8 and 2.0 angstroms resolution,
respectively. The trapped photoproduct corresponds to the late M state in the
transport cycle-that is, after proton transfer to Asp85 and release of a proton
to the extracellular membrane surface, but before reprotonation of the
deprotonated retinal Schiff base. Its density map describes displacements of
side chains near the retinal induced by its photoisomerization to 13-cis,15-anti
and an extensive rearrangement of the three-dimensional network of
hydrogen-bonded residues and bound water that accounts for the changed pKa
values (where Ka is the acid constant) of the Schiff base and Asp85. The
structural changes detected suggest the means for conserving energy at the
active site and for ensuring the directionality of proton translocation.
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Selected figure(s)
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Figure 2.
Fig. 2. View of retinal and the surrounding region (37). The
2F[o]  F[c]
electron density map of the M state contoured at 1  is shown
in blue. The corresponding M state atomic model is shown in
yellow. Also shown, for reference, is the atomic model of the BR
(ground) state in purple. The cytoplasmic half of the ion pump
is above the retinal, and the extracellular half is below the
retinal.
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Figure 3.
Fig. 3. Stereoviews of the structure and hydrogen bonding of
the extracellular region in the BR state (A) and the M state
(B). The extensive hydrogen-bonding network leading to the
extracellular surface found in the BR state is fragmented in the
M state. Notable are new hydrogen bonds formed in the M state
between Trp86 NE and Asp212 OD-1 and between Tyr83 OH and Glu194
OE-1; the carboxylate side chain of Asp85 has lost a hydrogen
bond from Thr89 OH; the guanidinium moiety of Arg82 has moved
away from the Schiff base and toward the extracellular side
(downward) by 1.7 Å, largely because of a rotation around
 [3] by
60°.
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The above figures are
reprinted
by permission from the AAAs:
Science
(1999,
286,
255-261)
copyright 1999.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Nakatsuma,
T.Yamashita,
K.Sasaki,
A.Kawanabe,
K.Inoue,
Y.Furutani,
Y.Shichida,
and
H.Kandori
(2011).
Chimeric microbial rhodopsins containing the third cytoplasmic loop of bovine rhodopsin.
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Biophys J,
100,
1874-1882.
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A.Möglich,
X.Yang,
R.A.Ayers,
and
K.Moffat
(2010).
Structure and function of plant photoreceptors.
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Annu Rev Plant Biol,
61,
21-47.
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J.A.Lundbaek,
S.A.Collingwood,
H.I.Ingólfsson,
R.Kapoor,
and
O.S.Andersen
(2010).
Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes.
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J R Soc Interface,
7,
373-395.
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M.Shibata,
H.Yamashita,
T.Uchihashi,
H.Kandori,
and
T.Ando
(2010).
High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin.
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Nat Nanotechnol,
5,
208-212.
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S.Westenhoff,
E.Nazarenko,
E.Malmerberg,
J.Davidsson,
G.Katona,
and
R.Neutze
(2010).
Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches.
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Acta Crystallogr A,
66,
207-219.
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A.Berndt,
O.Yizhar,
L.A.Gunaydin,
P.Hegemann,
and
K.Deisseroth
(2009).
Bi-stable neural state switches.
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Nat Neurosci,
12,
229-234.
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D.Chen,
and
J.K.Lanyi
(2009).
Structural changes in the N and N' states of the bacteriorhodopsin photocycle.
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Biophys J,
96,
2779-2788.
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M.C.Rheinstädter,
K.Schmalzl,
K.Wood,
and
D.Strauch
(2009).
Protein-protein interaction in purple membrane.
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Phys Rev Lett,
103,
128104.
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R.Tóth-Boconádi,
A.Dér,
L.Fábián,
S.G.Taneva,
and
L.Keszthelyi
(2009).
Excitation of the m intermediates of bacteriorhodopsin.
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Photochem Photobiol,
85,
609-613.
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T.Hirai,
and
S.Subramaniam
(2009).
Protein conformational changes in the bacteriorhodopsin photocycle: comparison of findings from electron and X-ray crystallographic analyses.
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PLoS One,
4,
e5769.
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T.Hirai,
S.Subramaniam,
and
J.K.Lanyi
(2009).
Structural snapshots of conformational changes in a seven-helix membrane protein: lessons from bacteriorhodopsin.
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Curr Opin Struct Biol,
19,
433-439.
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T.Y.Kim,
M.Moeller,
K.Winkler,
K.Kirchberg,
and
U.Alexiev
(2009).
Dissection of Environmental Changes at the Cytoplasmic Surface of Light-activated Bacteriorhodopsin and Visual Rhodopsin: Sequence of Spectrally Silent Steps.
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Photochem Photobiol,
85,
570-577.
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A.Chattopadhyay,
S.S.Rawat,
D.V.Greathouse,
D.A.Kelkar,
and
R.E.Koeppe
(2008).
Role of tryptophan residues in gramicidin channel organization and function.
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Biophys J,
95,
166-175.
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A.Damjanović,
X.Wu,
B.García-Moreno E,
and
B.R.Brooks
(2008).
Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study.
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Biophys J,
95,
4091-4101.
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H.Luecke,
B.Schobert,
J.Stagno,
E.S.Imasheva,
J.M.Wang,
S.P.Balashov,
and
J.K.Lanyi
(2008).
Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore.
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Proc Natl Acad Sci U S A,
105,
16561-16565.
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PDB code:
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K.Wood,
U.Lehnert,
B.Kessler,
G.Zaccai,
and
D.Oesterhelt
(2008).
Hydration dependence of active core fluctuations in bacteriorhodopsin.
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Biophys J,
95,
194-202.
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M.Andersson,
J.Vincent,
D.van der Spoel,
J.Davidsson,
and
R.Neutze
(2008).
A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins.
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Structure,
16,
21-28.
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P.Phatak,
N.Ghosh,
H.Yu,
Q.Cui,
and
M.Elstner
(2008).
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin.
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Proc Natl Acad Sci U S A,
105,
19672-19677.
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R.Hagedorn,
D.Gradmann,
and
P.Hegemann
(2008).
Dynamics of voltage profile in enzymatic ion transporters, demonstrated in electrokinetics of proton pumping rhodopsin.
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Biophys J,
95,
5005-5013.
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S.Braun-Sand,
P.K.Sharma,
Z.T.Chu,
A.V.Pisliakov,
and
A.Warshel
(2008).
The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all.
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Biochim Biophys Acta,
1777,
441-452.
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A.Seki,
S.Miyauchi,
S.Hayashi,
T.Kikukawa,
M.Kubo,
M.Demura,
V.Ganapathy,
and
N.Kamo
(2007).
Heterologous expression of Pharaonis halorhodopsin in Xenopus laevis oocytes and electrophysiological characterization of its light-driven Cl- pump activity.
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Biophys J,
92,
2559-2569.
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B.P.Kietis,
P.Saudargas,
G.Vàró,
and
L.Valkunas
(2007).
External electric control of the proton pumping in bacteriorhodopsin.
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Eur Biophys J,
36,
199-211.
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D.A.Karp,
A.G.Gittis,
M.R.Stahley,
C.A.Fitch,
W.E.Stites,
and
B.García-Moreno E
(2007).
High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp.
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Biophys J,
92,
2041-2053.
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PDB code:
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D.Chen,
J.M.Wang,
and
J.K.Lanyi
(2007).
Electron paramagnetic resonance study of structural changes in the O photointermediate of bacteriorhodopsin.
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J Mol Biol,
366,
790-805.
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J.K.Lanyi,
and
B.Schobert
(2007).
Structural changes in the L photointermediate of bacteriorhodopsin.
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J Mol Biol,
365,
1379-1392.
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PDB codes:
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J.Topolancik,
and
F.Vollmer
(2007).
Photoinduced transformations in bacteriorhodopsin membrane monitored with optical microcavities.
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Biophys J,
92,
2223-2229.
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L.Vogeley,
V.D.Trivedi,
O.A.Sineshchekov,
E.N.Spudich,
J.L.Spudich,
and
H.Luecke
(2007).
Crystal structure of the Anabaena sensory rhodopsin transducer.
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J Mol Biol,
367,
741-751.
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PDB codes:
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T.Yamashita,
and
K.Takatsuka
(2007).
Hydrogen-bond assisted enormous broadening of infrared spectra of phenol-water cationic cluster: an ab initio mixed quantum-classical study.
|
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J Chem Phys,
126,
074304.
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A.C.Johansson,
and
E.Lindahl
(2006).
Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations.
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Biophys J,
91,
4450-4463.
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A.Maeda,
J.E.Morgan,
R.B.Gennis,
and
T.G.Ebrey
(2006).
Water as a cofactor in the unidirectional light-driven proton transfer steps in bacteriorhodopsin.
|
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Photochem Photobiol,
82,
1398-1405.
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D.A.Kelkar,
and
A.Chattopadhyay
(2006).
Membrane interfacial localization of aromatic amino acids and membrane protein function.
|
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J Biosci,
31,
297-302.
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F.Garczarek,
and
K.Gerwert
(2006).
Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy.
|
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Nature,
439,
109-112.
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J.K.Lanyi,
and
B.Schobert
(2006).
Propagating structural perturbation inside bacteriorhodopsin: crystal structures of the M state and the D96A and T46V mutants.
|
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Biochemistry,
45,
12003-12010.
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PDB codes:
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M.Ming,
M.Lu,
S.P.Balashov,
T.G.Ebrey,
Q.Li,
and
J.Ding
(2006).
pH dependence of light-driven proton pumping by an archaerhodopsin from Tibet: comparison with bacteriorhodopsin.
|
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Biophys J,
90,
3322-3332.
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M.R.Gunner,
J.Mao,
Y.Song,
and
J.Kim
(2006).
Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations.
|
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Biochim Biophys Acta,
1757,
942-968.
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R.Tóth-Boconádi,
A.Dér,
S.G.Taneva,
and
L.Keszthelyi
(2006).
Excitation of the L intermediate of bacteriorhodopsin: electric responses to test x-ray structures.
|
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Biophys J,
90,
2651-2655.
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S.A.Hassan,
G.Hummer,
and
Y.S.Lee
(2006).
Effects of electric fields on proton transport through water chains.
|
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J Chem Phys,
124,
204510.
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S.P.Tsunoda,
D.Ewers,
S.Gazzarrini,
A.Moroni,
D.Gradmann,
and
P.Hegemann
(2006).
H+ -pumping rhodopsin from the marine alga Acetabularia.
|
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Biophys J,
91,
1471-1479.
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A.J.Mason,
G.J.Turner,
and
C.Glaubitz
(2005).
Conformational heterogeneity of transmembrane residues after the Schiff base reprotonation of bacteriorhodopsin: 15N CPMAS NMR of D85N/T170C membranes.
|
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FEBS J,
272,
2152-2164.
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A.M.Saxena,
J.B.Udgaonkar,
and
G.Krishnamoorthy
(2005).
Protein dynamics control proton transfer from bulk solvent to protein interior: a case study with a green fluorescent protein.
|
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Protein Sci,
14,
1787-1799.
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C.Kandt,
K.Gerwert,
and
J.Schlitter
(2005).
Water dynamics simulation as a tool for probing proton transfer pathways in a heptahelical membrane protein.
|
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Proteins,
58,
528-537.
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F.Garczarek,
L.S.Brown,
J.K.Lanyi,
and
K.Gerwert
(2005).
Proton binding within a membrane protein by a protonated water cluster.
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Proc Natl Acad Sci U S A,
102,
3633-3638.
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H.Kamikubo,
and
M.Kataoka
(2005).
Can the low-resolution structures of photointermediates of bacteriorhodopsin explain their crystal structures?
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Biophys J,
88,
1925-1931.
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H.Zheng,
J.Zhao,
S.Wang,
C.M.Lin,
T.Chen,
D.H.Jones,
C.Ma,
S.Opella,
and
X.Q.Xie
(2005).
Biosynthesis and purification of a hydrophobic peptide from transmembrane domains of G-protein-coupled CB2 receptor.
|
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J Pept Res,
65,
450-458.
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O.A.Sineshchekov,
E.G.Govorunova,
K.H.Jung,
S.Zauner,
U.G.Maier,
and
J.L.Spudich
(2005).
Rhodopsin-mediated photoreception in cryptophyte flagellates.
|
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Biophys J,
89,
4310-4319.
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P.Girard,
J.Prost,
and
P.Bassereau
(2005).
Passive or active fluctuations in membranes containing proteins.
|
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Phys Rev Lett,
94,
088102.
|
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S.Grudinin,
G.Büldt,
V.Gordeliy,
and
A.Baumgaertner
(2005).
Water molecules and hydrogen-bonded networks in bacteriorhodopsin--molecular dynamics simulations of the ground state and the M-intermediate.
|
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Biophys J,
88,
3252-3261.
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T.Oka,
K.Inoue,
M.Kataoka,
and
N.Yagi
(2005).
Structural transition of bacteriorhodopsin is preceded by deprotonation of Schiff base: microsecond time-resolved x-ray diffraction study of purple membrane.
|
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Biophys J,
88,
436-442.
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T.Sasaki,
M.Sonoyama,
M.Demura,
and
S.Mitaku
(2005).
Photobleaching of bacteriorhodopsin solubilized with triton X-100.
|
| |
Photochem Photobiol,
81,
1131-1137.
|
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V.Alexandrov,
U.Lehnert,
N.Echols,
D.Milburn,
D.Engelman,
and
M.Gerstein
(2005).
Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
|
| |
Protein Sci,
14,
633-643.
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X.W.Xu,
M.Wu,
and
W.D.Huang
(2005).
Isolation and characterization of a novel strain of Natrinema containing a bop gene.
|
| |
J Zhejiang Univ Sci B,
6,
142-146.
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B.L.Victor,
A.M.Baptista,
and
C.M.Soares
(2004).
Theoretical identification of proton channels in the quinol oxidase aa3 from Acidianus ambivalens.
|
| |
Biophys J,
87,
4316-4325.
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H.Jang,
P.S.Crozier,
M.J.Stevens,
and
T.B.Woolf
(2004).
How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation.
|
| |
Biophys J,
87,
129-145.
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J.A.Lundbaek,
P.Birn,
A.J.Hansen,
R.Søgaard,
C.Nielsen,
J.Girshman,
M.J.Bruno,
S.E.Tape,
J.Egebjerg,
D.V.Greathouse,
G.L.Mattice,
R.E.Koeppe,
and
O.S.Andersen
(2004).
Regulation of sodium channel function by bilayer elasticity: the importance of hydrophobic coupling. Effects of Micelle-forming amphiphiles and cholesterol.
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J Gen Physiol,
123,
599-621.
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J.K.Lanyi
(2004).
Bacteriorhodopsin.
|
| |
Annu Rev Physiol,
66,
665-688.
|
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M.Nakasako
(2004).
Water-protein interactions from high-resolution protein crystallography.
|
| |
Philos Trans R Soc Lond B Biol Sci,
359,
1191.
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M.T.Facciotti,
S.Rouhani-Manshadi,
and
R.M.Glaeser
(2004).
Energy transduction in transmembrane ion pumps.
|
| |
Trends Biochem Sci,
29,
445-451.
|
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Y.Ikeura,
K.Shimono,
M.Iwamoto,
Y.Sudo,
and
N.Kamo
(2004).
Role of Arg-72 of pharaonis Phoborhodopsin (sensory rhodopsin II) on its photochemistry.
|
| |
Biophys J,
86,
3112-3120.
|
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Y.Yokoyama,
M.Sonoyama,
and
S.Mitaku
(2004).
Inhomogeneous stability of bacteriorhodopsin in purple membrane against photobleaching at high temperature.
|
| |
Proteins,
54,
442-454.
|
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A.Maeda,
J.Herzfeld,
M.Belenky,
R.Needleman,
R.B.Gennis,
S.P.Balashov,
and
T.G.Ebrey
(2003).
Water-mediated hydrogen-bonded network on the cytoplasmic side of the Schiff base of the L photointermediate of bacteriorhodopsin.
|
| |
Biochemistry,
42,
14122-14129.
|
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Structure,
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PDB code:
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R.Renthal,
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Biophys J,
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Time-resolved x-ray diffraction reveals multiple conformations in the M-N transition of the bacteriorhodopsin photocycle.
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Where a reference describes a PDB structure, the PDB
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