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PDBsum entry 1d7e
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Photosynthesis
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PDB id
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1d7e
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Contents |
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* Residue conservation analysis
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DOI no:
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Protein Sci
9:64-72
(2000)
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PubMed id:
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Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.
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D.M.van Aalten,
W.Crielaard,
K.J.Hellingwerf,
L.Joshua-Tor.
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ABSTRACT
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The conformational changes during the photocycle of the photoactive yellow
protein have been the subject of many recent studies. Spectroscopic measurements
have shown that the photocycle also occurs in a crystalline environment, and
this has been the basis for subsequent Laue diffraction and cryocrystallographic
studies. These studies have shown that conformational changes during the
photocycle are limited to the chromophore and its immediate environment.
However, spectroscopic studies suggest the presence of large conformational
changes in the protein. Here, we address this apparent discrepancy in two ways.
First, we obtain a description of large concerted motions in the ground state of
the yellow protein from NMR data and theoretical calculations. Second, we
describe the high-resolution structure of the yellow protein crystallized in a
different space group. The structure of the yellow protein differs significantly
between the two crystal forms. We show that these differences can be used to
obtain a description of the flexibility of the protein that is consistent with
the motions observed in solution.
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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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Q.Zhao
(2009).
Protein thermodynamic structure.
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IUBMB Life,
61,
600-606.
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D.A.Kondrashov,
W.Zhang,
R.Aranda,
B.Stec,
and
G.N.Phillips
(2008).
Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments.
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Proteins,
70,
353-362.
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PDB codes:
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M.Kumauchi,
M.T.Hara,
P.Stalcup,
A.Xie,
and
W.D.Hoff
(2008).
Identification of six new photoactive yellow proteins--diversity and structure-function relationships in a bacterial blue light photoreceptor.
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Photochem Photobiol,
84,
956-969.
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M.H.Hefti,
K.J.Françoijs,
S.C.de Vries,
R.Dixon,
and
J.Vervoort
(2004).
The PAS fold. A redefinition of the PAS domain based upon structural prediction.
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Eur J Biochem,
271,
1198-1208.
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M.Sugishima,
N.Tanimoto,
K.Soda,
N.Hamada,
F.Tokunaga,
and
K.Fukuyama
(2004).
Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2 A resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP.
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Acta Crystallogr D Biol Crystallogr,
60,
2305-2309.
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PDB code:
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S.Anderson,
S.Crosson,
and
K.Moffat
(2004).
Short hydrogen bonds in photoactive yellow protein.
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Acta Crystallogr D Biol Crystallogr,
60,
1008-1016.
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PDB codes:
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Z.Kovári,
and
M.Vas
(2004).
Protein conformer selection by sequence-dependent packing contacts in crystals of 3-phosphoglycerate kinase.
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Proteins,
55,
198-209.
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A.Merlino,
L.Vitagliano,
M.A.Ceruso,
and
L.Mazzarella
(2003).
Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.
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Proteins,
53,
101-110.
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E.Chen,
T.Gensch,
A.B.Gross,
J.Hendriks,
K.J.Hellingwerf,
and
D.S.Kliger
(2003).
Dynamics of protein and chromophore structural changes in the photocycle of photoactive yellow protein monitored by time-resolved optical rotatory dispersion.
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Biochemistry,
42,
2062-2071.
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M.A.Cusanovich,
and
T.E.Meyer
(2003).
Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism.
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Biochemistry,
42,
4759-4770.
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R.Kort,
R.B.Ravelli,
F.Schotte,
D.Bourgeois,
W.Crielaard,
K.J.Hellingwerf,
and
M.Wulff
(2003).
Characterization of photocycle intermediates in crystalline photoactive yellow protein.
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Photochem Photobiol,
78,
131-137.
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S.Rajagopal,
and
K.Moffat
(2003).
Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction.
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Proc Natl Acad Sci U S A,
100,
1649-1654.
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PDB code:
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D.M.van Aalten,
W.Crielaard,
K.J.Hellingwerf,
and
L.Joshua-Tor
(2002).
Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution.
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Acta Crystallogr D Biol Crystallogr,
58,
585-590.
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
