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PDBsum entry 1i6a
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Transcription
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PDB id
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1i6a
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Contents |
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* Residue conservation analysis
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DOI no:
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Cell
105:103-113
(2001)
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PubMed id:
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Structural basis of the redox switch in the OxyR transcription factor.
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H.Choi,
S.Kim,
P.Mukhopadhyay,
S.Cho,
J.Woo,
G.Storz,
S.Ryu.
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ABSTRACT
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The Escherichia coli OxyR transcription factor senses H2O2 and is activated
through the formation of an intramolecular disulfide bond. Here we present the
crystal structures of the regulatory domain of OxyR in its reduced and oxidized
forms, determined at 2.7 A and 2.3 A resolutions, respectively. In the reduced
form, the two redox-active cysteines are separated by approximately 17 A.
Disulfide bond formation in the oxidized form results in a significant
structural change in the regulatory domain. The structural remodeling, which
leads to different oligomeric associations, accounts for the redox-dependent
switch in OxyR and provides a novel example of protein regulation by "fold
editing" through a reversible disulfide bond formation within a folded
domain.
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Selected figure(s)
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Figure 2.
Figure 2. Structural Transition within MonomerThe
environment of the redox-active cysteines in the reduced (A) and
oxidized (B) forms of OxyR. The redox-active cysteines Cys-199
(Ser-199 in the reduced form) and Cys-208, and the neighboring
residues, are shown in a ball-and-stick representation on a
ribbon diagram of the region. The point of view is approximately
from the left side of the monomers presented in Figure 1
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Figure 3.
Figure 3. Electron Density Maps of the Redox-Active
Cysteine RegionThe 2Fo−Fc maps of the reduced (A) and oxidized
(B) forms are superposed with the refined models. The maps are
contoured at a 0.9 σ level
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2001,
105,
103-113)
copyright 2001.
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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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B.C.An,
S.S.Lee,
E.M.Lee,
J.T.Lee,
S.G.Wi,
H.S.Jung,
W.Park,
S.Y.Lee,
and
B.Y.Chung
(2011).
Functional switching of a novel prokaryotic 2-Cys peroxiredoxin (PpPrx) under oxidative stress.
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Cell Stress Chaperones,
16,
317-328.
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H.Antelmann,
and
J.D.Helmann
(2011).
Thiol-based redox switches and gene regulation.
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Antioxid Redox Signal,
14,
1049-1063.
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J.M.Sobota,
and
J.A.Imlay
(2011).
Iron enzyme ribulose-5-phosphate 3-epimerase in Escherichia coli is rapidly damaged by hydrogen peroxide but can be protected by manganese.
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Proc Natl Acad Sci U S A,
108,
5402-5407.
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P.R.Chen,
P.Brugarolas,
and
C.He
(2011).
Redox signaling in human pathogens.
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Antioxid Redox Signal,
14,
1107-1118.
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S.J.Swanson,
W.G.Choi,
A.Chanoca,
and
S.Gilroy
(2011).
In vivo imaging of Ca2+, pH, and reactive oxygen species using fluorescent probes in plants.
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| |
Annu Rev Plant Biol,
62,
273-297.
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Z.Liu,
M.Yang,
G.L.Peterfreund,
A.M.Tsou,
N.Selamoglu,
F.Daldal,
Z.Zhong,
B.Kan,
and
J.Zhu
(2011).
Vibrio cholerae anaerobic induction of virulence gene expression is controlled by thiol-based switches of virulence regulator AphB.
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Proc Natl Acad Sci U S A,
108,
810-815.
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A.J.Meyer,
and
T.P.Dick
(2010).
Fluorescent protein-based redox probes.
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Antioxid Redox Signal,
13,
621-650.
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B.C.An,
S.S.Lee,
E.M.Lee,
S.G.Wi,
W.Park,
and
B.Y.Chung
(2010).
Global analysis of disulfide bond proteins in Pseudomonas aeruginosa exposed to hydrogen peroxide and gamma rays.
|
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Int J Radiat Biol,
86,
400-408.
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|
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B.Enyedi,
P.Várnai,
and
M.Geiszt
(2010).
Redox state of the endoplasmic reticulum is controlled by Ero1L-alpha and intraluminal calcium.
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Antioxid Redox Signal,
13,
721-729.
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G.S.Knapp,
and
J.C.Hu
(2010).
Specificity of the E. coli LysR-type transcriptional regulators.
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PLoS One,
5,
e15189.
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H.Chen,
C.Yi,
J.Zhang,
W.Zhang,
Z.Ge,
C.G.Yang,
and
C.He
(2010).
Structural insight into the oxidation-sensing mechanism of the antibiotic resistance of regulator MexR.
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EMBO Rep,
11,
685-690.
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PDB code:
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H.Yang,
G.L.Lipscomb,
A.M.Keese,
G.J.Schut,
M.Thomm,
M.W.Adams,
B.C.Wang,
and
R.A.Scott
(2010).
SurR regulates hydrogen production in Pyrococcus furiosus by a sulfur-dependent redox switch.
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Mol Microbiol,
77,
1111-1122.
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K.J.McLaughlin,
C.M.Strain-Damerell,
K.Xie,
D.Brekasis,
A.S.Soares,
M.S.Paget,
and
C.L.Kielkopf
(2010).
Structural basis for NADH/NAD+ redox sensing by a Rex family repressor.
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Mol Cell,
38,
563-575.
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PDB codes:
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L.Yin,
L.Wang,
H.Lu,
G.Xu,
H.Chen,
H.Zhan,
B.Tian,
and
Y.Hua
(2010).
DRA0336, another OxyR homolog, involved in the antioxidation mechanisms in Deinococcus radiodurans.
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J Microbiol,
48,
473-479.
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M.A.Wouters,
S.W.Fan,
and
N.L.Haworth
(2010).
Disulfides as redox switches: from molecular mechanisms to functional significance.
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Antioxid Redox Signal,
12,
53-91.
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S.Sainsbury,
J.Ren,
J.E.Nettleship,
N.J.Saunders,
D.I.Stuart,
and
R.J.Owens
(2010).
The structure of a reduced form of OxyR from Neisseria meningitidis.
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BMC Struct Biol,
10,
10.
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PDB code:
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V.Duarte,
and
J.M.Latour
(2010).
PerR vs OhrR: selective peroxide sensing in Bacillus subtilis.
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Mol Biosyst,
6,
316-323.
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Y.J.Yang,
P.F.Wu,
L.H.Long,
D.F.Yu,
W.N.Wu,
Z.L.Hu,
H.Fu,
N.Xie,
Y.Jin,
L.Ni,
J.Z.Wang,
F.Wang,
and
J.G.Chen
(2010).
Reversal of aging-associated hippocampal synaptic plasticity deficits by reductants via regulation of thiol redox and NMDA receptor function.
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Aging Cell,
9,
709-721.
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Z.Wang,
Z.Zhou,
Z.Y.Guo,
and
C.W.Chi
(2010).
Snapshot of the interaction between HIV envelope glycoprotein 120 and protein disulfide isomerase.
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Acta Biochim Biophys Sin (Shanghai),
42,
358-362.
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D.A.Traoré,
A.El Ghazouani,
L.Jacquamet,
F.Borel,
J.L.Ferrer,
D.Lascoux,
J.L.Ravanat,
M.Jaquinod,
G.Blondin,
C.Caux-Thang,
V.Duarte,
and
J.M.Latour
(2009).
Structural and functional characterization of 2-oxo-histidine in oxidized PerR protein.
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Nat Chem Biol,
5,
53-59.
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PDB code:
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G.S.Knapp,
and
J.C.Hu
(2009).
The oligomerization of CynR in Escherichia coli.
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Protein Sci,
18,
2307-2315.
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G.S.Knapp,
J.W.Tsai,
and
J.C.Hu
(2009).
The oligomerization of OxyR in Escherichia coli.
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Protein Sci,
18,
101-107.
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G.V.Smirnova,
Z.Y.Samoylova,
N.G.Muzyka,
and
O.N.Oktyabrsky
(2009).
Influence of polyphenols on Escherichia coli resistance to oxidative stress.
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Free Radic Biol Med,
46,
759-768.
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K.S.Jensen,
R.E.Hansen,
and
J.R.Winther
(2009).
Kinetic and thermodynamic aspects of cellular thiol-disulfide redox regulation.
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Antioxid Redox Signal,
11,
1047-1058.
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L.K.Wood,
and
D.J.Thiele
(2009).
Transcriptional activation in yeast in response to copper deficiency involves copper-zinc superoxide dismutase.
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J Biol Chem,
284,
404-413.
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P.R.Chen,
S.Nishida,
C.B.Poor,
A.Cheng,
T.Bae,
L.Kuechenmeister,
P.M.Dunman,
D.Missiakas,
and
C.He
(2009).
A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus.
|
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Mol Microbiol,
71,
198-211.
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S.H.Craven,
O.C.Ezezika,
S.Haddad,
R.A.Hall,
C.Momany,
and
E.L.Neidle
(2009).
Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.
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Mol Microbiol,
72,
881-894.
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PDB codes:
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S.Sainsbury,
L.A.Lane,
J.Ren,
R.J.Gilbert,
N.J.Saunders,
C.V.Robinson,
D.I.Stuart,
and
R.J.Owens
(2009).
The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators.
|
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Nucleic Acids Res,
37,
4545-4558.
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PDB codes:
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S.W.Fan,
R.A.George,
N.L.Haworth,
L.L.Feng,
J.Y.Liu,
and
M.A.Wouters
(2009).
Conformational changes in redox pairs of protein structures.
|
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Protein Sci,
18,
1745-1765.
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|
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Y.G.Kim,
S.Lee,
O.S.Kwon,
S.Y.Park,
S.J.Lee,
B.J.Park,
and
K.J.Kim
(2009).
Redox-switch modulation of human SSADH by dynamic catalytic loop.
|
| |
EMBO J,
28,
959-968.
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PDB codes:
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Z.Ma,
F.E.Jacobsen,
and
D.P.Giedroc
(2009).
Coordination chemistry of bacterial metal transport and sensing.
|
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Chem Rev,
109,
4644-4681.
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Z.Xu,
H.Y.Chan,
W.L.Lam,
K.H.Lam,
L.S.Lam,
T.B.Ng,
and
S.W.Au
(2009).
SUMO proteases: redox regulation and biological consequences.
|
| |
Antioxid Redox Signal,
11,
1453-1484.
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C.C.Winterbourn
(2008).
Reconciling the chemistry and biology of reactive oxygen species.
|
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Nat Chem Biol,
4,
278-286.
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C.C.Winterbourn,
and
M.B.Hampton
(2008).
Thiol chemistry and specificity in redox signaling.
|
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Free Radic Biol Med,
45,
549-561.
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|
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C.Passarelli,
S.Petrini,
A.Pastore,
V.Bonetto,
P.Sale,
L.M.Gaeta,
G.Tozzi,
E.Bertini,
M.Canepari,
R.Rossi,
and
F.Piemonte
(2008).
Myosin as a potential redox-sensor: an in vitro study.
|
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J Muscle Res Cell Motil,
29,
119-126.
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F.R.Salsbury,
S.T.Knutson,
L.B.Poole,
and
J.S.Fetrow
(2008).
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid.
|
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Protein Sci,
17,
299-312.
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H.Chen,
G.Xu,
Y.Zhao,
B.Tian,
H.Lu,
X.Yu,
Z.Xu,
N.Ying,
S.Hu,
and
Y.Hua
(2008).
A novel OxyR sensor and regulator of hydrogen peroxide stress with one cysteine residue in Deinococcus radiodurans.
|
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PLoS ONE,
3,
e1602.
|
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H.Chen,
J.Hu,
P.R.Chen,
L.Lan,
Z.Li,
L.M.Hicks,
A.R.Dinner,
and
C.He
(2008).
The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism.
|
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Proc Natl Acad Sci U S A,
105,
13586-13591.
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J.A.Imlay
(2008).
Cellular defenses against superoxide and hydrogen peroxide.
|
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Annu Rev Biochem,
77,
755-776.
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J.J.LeBlanc,
A.K.Brassinga,
F.Ewann,
R.J.Davidson,
and
P.S.Hoffman
(2008).
An ortholog of OxyR in Legionella pneumophila is expressed postexponentially and negatively regulates the alkyl hydroperoxide reductase (ahpC2D) operon.
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J Bacteriol,
190,
3444-3455.
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R.Ieva,
D.Roncarati,
M.M.Metruccio,
K.L.Seib,
V.Scarlato,
and
I.Delany
(2008).
OxyR tightly regulates catalase expression in Neisseria meningitidis through both repression and activation mechanisms.
|
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Mol Microbiol,
70,
1152-1165.
|
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R.R.Thangudu,
M.Manoharan,
N.Srinivasan,
F.Cadet,
R.Sowdhamini,
and
B.Offmann
(2008).
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families.
|
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BMC Struct Biol,
8,
55.
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|
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R.Sanchez,
M.Riddle,
J.Woo,
and
J.Momand
(2008).
Prediction of reversibly oxidized protein cysteine thiols using protein structure properties.
|
| |
Protein Sci,
17,
473-481.
|
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|
|
|
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S.Sainsbury,
J.Ren,
N.J.Saunders,
D.I.Stuart,
and
R.J.Owens
(2008).
Crystallization and preliminary X-ray analysis of CrgA, a LysR-type transcriptional regulator from pathogenic Neisseria meningitidis MC58.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
797-801.
|
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|
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Y.Guo,
L.Chen,
L.Yang,
and
Q.Wang
(2008).
Counting sulfhydryls and disulfide bonds in peptides and proteins using mercurial ions as an MS-tag.
|
| |
J Am Soc Mass Spectrom,
19,
1108-1113.
|
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|
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Y.M.Janssen-Heininger,
B.T.Mossman,
N.H.Heintz,
H.J.Forman,
B.Kalyanaraman,
T.Finkel,
J.S.Stamler,
S.G.Rhee,
and
A.van der Vliet
(2008).
Redox-based regulation of signal transduction: principles, pitfalls, and promises.
|
| |
Free Radic Biol Med,
45,
1.
|
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Y.Yamazaki,
H.Fukusumi,
H.Kamikubo,
and
M.Kataoka
(2008).
Role of the N-terminal region in the function of the photosynthetic bacterium transcription regulator PpsR.
|
| |
Photochem Photobiol,
84,
839-844.
|
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|
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A.Harrison,
W.C.Ray,
B.D.Baker,
D.W.Armbruster,
L.O.Bakaletz,
and
R.S.Munson
(2007).
The OxyR regulon in nontypeable Haemophilus influenzae.
|
| |
J Bacteriol,
189,
1004-1012.
|
|
|
|
|
|
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B.D'Autréaux,
and
M.B.Toledano
(2007).
ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis.
|
| |
Nat Rev Mol Cell Biol,
8,
813-824.
|
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|
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C.M.Sanders,
D.Sizov,
P.R.Seavers,
M.Ortiz-Lombardía,
and
A.A.Antson
(2007).
Transcription activator structure reveals redox control of a replication initiation reaction.
|
| |
Nucleic Acids Res,
35,
3504-3515.
|
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PDB codes:
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E.A.Veal,
A.M.Day,
and
B.A.Morgan
(2007).
Hydrogen peroxide sensing and signaling.
|
| |
Mol Cell,
26,
1.
|
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H.Takahashi,
Y.Shin,
S.J.Cho,
W.M.Zago,
T.Nakamura,
Z.Gu,
Y.Ma,
H.Furukawa,
R.Liddington,
D.Zhang,
G.Tong,
H.S.Chen,
and
S.A.Lipton
(2007).
Hypoxia enhances S-nitrosylation-mediated NMDA receptor inhibition via a thiol oxygen sensor motif.
|
| |
Neuron,
53,
53-64.
|
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|
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K.J.Newberry,
M.Fuangthong,
W.Panmanee,
S.Mongkolsuk,
and
R.G.Brennan
(2007).
Structural mechanism of organic hydroperoxide induction of the transcription regulator OhrR.
|
| |
Mol Cell,
28,
652-664.
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PDB codes:
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K.Piotukh,
D.Kosslick,
J.Zimmermann,
E.Krause,
and
C.Freund
(2007).
Reversible disulfide bond formation of intracellular proteins probed by NMR spectroscopy.
|
| |
Free Radic Biol Med,
43,
1263-1270.
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L.H.Ma,
C.L.Takanishi,
and
M.J.Wood
(2007).
Molecular mechanism of oxidative stress perception by the Orp1 protein.
|
| |
J Biol Chem,
282,
31429-31436.
|
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M.Giorgio,
M.Trinei,
E.Migliaccio,
and
P.G.Pelicci
(2007).
Hydrogen peroxide: a metabolic by-product or a common mediator of ageing signals?
|
| |
Nat Rev Mol Cell Biol,
8,
722-728.
|
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O.C.Ezezika,
S.Haddad,
E.L.Neidle,
and
C.Momany
(2007).
Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
361-368.
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PDB codes:
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|
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O.N.Oktyabrsky,
and
G.V.Smirnova
(2007).
Redox regulation of cellular functions.
|
| |
Biochemistry (Mosc),
72,
132-145.
|
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|
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S.Soonsanga,
M.Fuangthong,
and
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5493-5504.
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PDB code:
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J.Nordberg,
and
E.S.Arnér
(2001).
Reactive oxygen species, antioxidants, and the mammalian thioredoxin system.
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Free Radic Biol Med,
31,
1287-1312.
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J.S.Stamler,
S.Lamas,
and
F.C.Fang
(2001).
Nitrosylation. the prototypic redox-based signaling mechanism.
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Cell,
106,
675-683.
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S.Ehrt,
D.Schnappinger,
S.Bekiranov,
J.Drenkow,
S.Shi,
T.R.Gingeras,
T.Gaasterland,
G.Schoolnik,
and
C.Nathan
(2001).
Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase.
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J Exp Med,
194,
1123-1140.
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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
code is
shown on the right.
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Links
