 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Photoreceptor
|
PDB id
|
|
|
|
1s1y
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
Gene Ontology (GO) functional annotation
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Biological process
|
response to stimulus
|
5 terms
|
|
|
Biochemical function
|
signal transducer activity
|
3 terms
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Structure
12:1039-1045
(2004)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein.
|
|
S.Anderson,
V.Srajer,
R.Pahl,
S.Rajagopal,
F.Schotte,
P.Anfinrud,
M.Wulff,
K.Moffat.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
We use time-resolved crystallography to observe the structural progression of a
bacterial blue light photoreceptor throughout its photocycle. Data were
collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of
photoactive yellow protein. Refinement of transient chromophore conformations
shows that the spectroscopically distinct intermediates are formed via
progressive disruption of the hydrogen bond network to the chromophore. Although
structural change occurs within a few nanoseconds on and around the chromophore,
it takes milliseconds for a distinct pattern of tertiary structural change to
fully progress through the entire molecule, thus generating the putative
signaling state. Remarkably, the coupling between the chromophore conformation
and the tertiary structure of this small protein is not tight: there are leads
and lags between changes in the conformation of the chromophore and the protein
tertiary structure.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
Figure 5.
Figure 5. Chromophore Conformations in the pR and pB
IntermediatesDifference electron density maps (A and B) and
electron density maps (C and D) for the pR and pB chromophore
conformations, derived from the two highly averaged data sets
(Table 2). Difference electron density contoured at ±2s and
±3.5s, for the (A) pR and (B) pB states. Electron density maps
contoured at ±1s and ±3s; yellow atomic model, ground-state
conformation; orange models, chromophore conformations for the
(C) pR and (D) pB states.
|
|
|
|
|
|
| |
The above figure is
reprinted
by permission from Cell Press:
Structure
(2004,
12,
1039-1045)
copyright 2004.
|
|
| |
Figure was
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
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.
|
| |
Acta Crystallogr A, 66,
207-219.
|
|
|
|
|
|
|
A.Specht,
F.Bolze,
Z.Omran,
J.F.Nicoud,
and
M.Goeldner
(2009).
Photochemical tools to study dynamic biological processes.
|
| |
HFSP J, 3,
255-264.
|
|
|
|
|
|
|
J.Hendriks,
and
K.J.Hellingwerf
(2009).
pH Dependence of the Photoactive Yellow Protein Photocycle Recovery Reaction Reveals a New Late Photocycle Intermediate with a Deprotonated Chromophore.
|
| |
J Biol Chem, 284,
5277-5288.
|
|
|
|
|
|
|
M.Chergui,
and
A.H.Zewail
(2009).
Electron and X-ray methods of ultrafast structural dynamics: advances and applications.
|
| |
Chemphyschem, 10,
28-43.
|
|
|
|
|
|
|
R.L.Owen,
A.R.Pearson,
A.Meents,
P.Boehler,
V.Thominet,
and
C.Schulze-Briese
(2009).
A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source.
|
| |
J Synchrotron Radiat, 16,
173-182.
|
|
|
|
|
|
|
N.Shimizu,
Y.Imamoto,
M.Harigai,
H.Kamikubo,
Y.Yamazaki,
and
M.Kataoka
(2006).
pH-dependent equilibrium between long lived near-UV intermediates of photoactive yellow protein.
|
| |
J Biol Chem, 281,
4318-4325.
|
|
|
|
|
|
|
R.Brudler,
C.R.Gessner,
S.Li,
S.Tyndall,
E.D.Getzoff,
and
V.L.Woods
(2006).
PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry.
|
| |
J Mol Biol, 363,
148-160.
|
|
|
|
|
|
|
S.Yeremenko,
I.H.van Stokkum,
K.Moffat,
and
K.J.Hellingwerf
(2006).
Influence of the crystalline state on photoinduced dynamics of photoactive yellow protein studied by ultraviolet-visible transient absorption spectroscopy.
|
| |
Biophys J, 90,
4224-4235.
|
|
|
|
|
|
|
D.Bourgeois,
and
A.Royant
(2005).
Advances in kinetic protein crystallography.
|
| |
Curr Opin Struct Biol, 15,
538-547.
|
|
|
|
|
|
|
J.Vreede,
W.Crielaard,
K.J.Hellingwerf,
and
P.G.Bolhuis
(2005).
Predicting the signaling state of photoactive yellow protein.
|
| |
Biophys J, 88,
3525-3535.
|
|
|
|
|
|
|
M.A.van der Horst,
W.Laan,
S.Yeremenko,
A.Wende,
P.Palm,
D.Oesterhelt,
and
K.J.Hellingwerf
(2005).
From primary photochemistry to biological function in the blue-light photoreceptors PYP and AppA.
|
| |
Photochem Photobiol Sci, 4,
688-693.
|
|
|
|
|
|
|
S.Rajagopal,
S.Anderson,
V.Srajer,
M.Schmidt,
R.Pahl,
and
K.Moffat
(2005).
A structural pathway for signaling in the E46Q mutant of photoactive yellow protein.
|
| |
Structure, 13,
55-63.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Yeremenko,
and
K.J.Hellingwerf
(2005).
Resolving protein structure dynamically.
|
| |
Structure, 13,
4-6.
|
|
|
|
|
|
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.
|
|
Links
