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PDBsum entry 1z91
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DNA binding protein
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PDB id
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1z91
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Contents |
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* Residue conservation analysis
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DOI no:
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Mol Cell
20:131-141
(2005)
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PubMed id:
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Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family.
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M.Hong,
M.Fuangthong,
J.D.Helmann,
R.G.Brennan.
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ABSTRACT
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The mechanisms by which Bacillus subtilis OhrR, a member of the MarR family of
transcription regulators, binds the ohrA operator and is induced by oxidation of
its lone cysteine residue by organic hydroperoxides to sulphenic acid are
unknown. Here, we describe the crystal structures of reduced OhrR and an
OhrR-ohrA operator complex. To bind DNA, OhrR employs a chimeric winged
helix-turn-helix DNA binding motif, which is composed of extended
eukaryotic-like wings, prokaryotic helix-turn-helix motifs, and helix-helix
elements. The reactivity of the peroxide-sensing cysteine is not modulated by
proximal basic residues but largely by the positive dipole of helix alpha1.
Induction originates from the alleviation of intersubunit steric clash between
the sulphenic acid moieties of the oxidized sensor cysteines and nearby
tyrosines and methionines. The structure of the OhrR-ohrA operator complex
reveals the DNA binding mechanism of the entire MarR family and suggests a
common inducer binding pocket.
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Selected figure(s)
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Figure 2.
Figure 2. Structure of the OhrR-ohrA Operator Complex
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Figure 3.
Figure 3. OhrR-ohrA Operator Binding
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(2005,
20,
131-141)
copyright 2005.
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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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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.Lin,
T.Zhou,
and
J.Wang
(2011).
Solution structure of the human HSPC280 protein.
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Protein Sci,
20,
216-223.
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PDB code:
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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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A.P.Zhang,
Y.Z.Pigli,
and
P.A.Rice
(2010).
Structure of the LexA-DNA complex and implications for SOS box measurement.
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Nature,
466,
883-886.
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PDB codes:
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C.Andrésen,
S.Jalal,
D.Aili,
Y.Wang,
S.Islam,
A.Jarl,
B.Liedberg,
B.Wretlind,
L.G.Mårtensson,
and
M.Sunnerhagen
(2010).
Critical biophysical properties in the Pseudomonas aeruginosa efflux gene regulator MexR are targeted by mutations conferring multidrug resistance.
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Protein Sci,
19,
680-692.
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D.Chaix,
M.L.Ferguson,
C.Atmanene,
A.Van Dorsselaer,
S.Sanglier-Cianférani,
C.A.Royer,
and
N.Declerck
(2010).
Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex.
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Nucleic Acids Res,
38,
5944-5957.
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I.C.Perera,
and
A.Grove
(2010).
Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators.
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J Mol Cell Biol,
2,
243-254.
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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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R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
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Annu Rev Biochem,
79,
233-269.
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S.Atichartpongkul,
M.Fuangthong,
P.Vattanaviboon,
and
S.Mongkolsuk
(2010).
Analyses of the regulatory mechanism and physiological roles of Pseudomonas aeruginosa OhrR, a transcription regulator and a sensor of organic hydroperoxides.
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J Bacteriol,
192,
2093-2101.
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S.R.Geiger,
K.Lorenzen,
A.Schreieck,
P.Hanecker,
D.Kostrewa,
A.J.Heck,
and
P.Cramer
(2010).
RNA polymerase I contains a TFIIF-related DNA-binding subcomplex.
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Mol Cell,
39,
583-594.
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PDB codes:
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S.Schielke,
M.Frosch,
and
O.Kurzai
(2010).
Virulence determinants involved in differential host niche adaptation of Neisseria meningitidis and Neisseria gonorrhoeae.
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Med Microbiol Immunol,
199,
185-196.
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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.M.Chang,
W.Y.Jeng,
T.P.Ko,
Y.J.Yeh,
C.K.Chen,
and
A.H.Wang
(2010).
Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis.
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Proc Natl Acad Sci U S A,
107,
8617-8622.
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PDB codes:
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Z.Liu,
T.A.Walton,
and
D.C.Rees
(2010).
A reported archaeal mechanosensitive channel is a structural homolog of MarR-like transcriptional regulators.
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Protein Sci,
19,
808-814.
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PDB code:
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C.B.Poor,
P.R.Chen,
E.Duguid,
P.A.Rice,
and
C.He
(2009).
Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus.
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J Biol Chem,
284,
23517-23524.
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PDB codes:
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C.E.Nichols,
S.Sainsbury,
J.Ren,
T.S.Walter,
A.Verma,
D.K.Stammers,
N.J.Saunders,
and
R.J.Owens
(2009).
The structure of NMB1585, a MarR-family regulator from Neisseria meningitidis.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
204-209.
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PDB code:
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D.P.Giedroc
(2009).
Hydrogen peroxide sensing in Bacillus subtilis: it is all about the (metallo)regulator.
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Mol Microbiol,
73,
1-4.
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K.Hirooka,
Y.Danjo,
Y.Hanano,
S.Kunikane,
H.Matsuoka,
S.Tojo,
and
Y.Fujita
(2009).
Regulation of the Bacillus subtilis divergent yetL and yetM genes by a transcriptional repressor, YetL, in response to flavonoids.
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J Bacteriol,
191,
3685-3697.
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L.Jacquamet,
D.A.Traoré,
J.L.Ferrer,
O.Proux,
D.Testemale,
J.L.Hazemann,
E.Nazarenko,
A.El Ghazouani,
C.Caux-Thang,
V.Duarte,
and
J.M.Latour
(2009).
Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding.
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Mol Microbiol,
73,
20-31.
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PDB code:
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M.Kumaraswami,
J.T.Schuman,
S.M.Seo,
G.W.Kaatz,
and
R.G.Brennan
(2009).
Structural and biochemical characterization of MepR, a multidrug binding transcription regulator of the Staphylococcus aureus multidrug efflux pump MepA.
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Nucleic Acids Res,
37,
1211-1224.
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PDB code:
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O.K.Kim,
L.K.Garrity-Ryan,
V.J.Bartlett,
M.C.Grier,
A.K.Verma,
G.Medjanis,
J.E.Donatelli,
A.B.Macone,
S.K.Tanaka,
S.B.Levy,
and
M.N.Alekshun
(2009).
N-hydroxybenzimidazole inhibitors of the transcription factor LcrF in Yersinia: novel antivirulence agents.
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J Med Chem,
52,
5626-5634.
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P.K.Madoori,
H.Agustiandari,
A.J.Driessen,
and
A.M.Thunnissen
(2009).
Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition.
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EMBO J,
28,
156-166.
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PDB codes:
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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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P.Zuber
(2009).
Management of oxidative stress in Bacillus.
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Annu Rev Microbiol,
63,
575-597.
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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.Schielke,
C.Huebner,
C.Spatz,
V.Nägele,
N.Ackermann,
M.Frosch,
O.Kurzai,
and
A.Schubert-Unkmeir
(2009).
Expression of the meningococcal adhesin NadA is controlled by a transcriptional regulator of the MarR family.
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Mol Microbiol,
72,
1054-1067.
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T.Kumarevel,
T.Tanaka,
T.Umehara,
and
S.Yokoyama
(2009).
ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.
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Nucleic Acids Res,
37,
4723-4735.
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PDB codes:
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W.Eiamphungporn,
S.Soonsanga,
J.W.Lee,
and
J.D.Helmann
(2009).
Oxidation of a single active site suffices for the functional inactivation of the dimeric Bacillus subtilis OhrR repressor in vitro.
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Nucleic Acids Res,
37,
1174-1181.
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Y.M.Zhang,
and
C.O.Rock
(2009).
Transcriptional regulation in bacterial membrane lipid synthesis.
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J Lipid Res,
50,
S115-S119.
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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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A.L.Cheung,
K.Nishina,
and
A.C.Manna
(2008).
SarA of Staphylococcus aureus binds to the sarA promoter to regulate gene expression.
|
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J Bacteriol,
190,
2239-2243.
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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.R.Wallen,
C.Paige,
T.C.Mallett,
P.A.Karplus,
and
A.Claiborne
(2008).
Pyridine nucleotide complexes with Bacillus anthracis coenzyme A-disulfide reductase: a structural analysis of dual NAD(P)H specificity.
|
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Biochemistry,
47,
5182-5193.
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PDB codes:
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M.Leelakriangsak,
N.T.Huyen,
S.Töwe,
N.van Duy,
D.Becher,
M.Hecker,
H.Antelmann,
and
P.Zuber
(2008).
Regulation of quinone detoxification by the thiol stress sensing DUF24/MarR-like repressor, YodB in Bacillus subtilis.
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Mol Microbiol,
67,
1108-1124.
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M.S.Wilke,
M.Heller,
A.L.Creagh,
C.A.Haynes,
L.P.McIntosh,
K.Poole,
and
N.C.Strynadka
(2008).
The crystal structure of MexR from Pseudomonas aeruginosa in complex with its antirepressor ArmR.
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Proc Natl Acad Sci U S A,
105,
14832-14837.
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PDB code:
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S.Soonsanga,
J.W.Lee,
and
J.D.Helmann
(2008).
Conversion of Bacillus subtilis OhrR from a 1-Cys to a 2-Cys peroxide sensor.
|
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J Bacteriol,
190,
5738-5745.
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B.D'Autréaux,
and
M.B.Toledano
(2007).
ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis.
|
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Nat Rev Mol Cell Biol,
8,
813-824.
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C.E.Stevenson,
H.Kock,
S.Mootien,
S.C.Davies,
M.J.Bibb,
and
D.M.Lawson
(2007).
Crystallization and preliminary X-ray analysis of AbsC, a novel regulator of antibiotic production in Streptomyces coelicolor.
|
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
233-235.
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D.M.Daigle,
L.Cao,
S.Fraud,
M.S.Wilke,
A.Pacey,
R.Klinoski,
N.C.Strynadka,
C.R.Dean,
and
K.Poole
(2007).
Protein modulator of multidrug efflux gene expression in Pseudomonas aeruginosa.
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J Bacteriol,
189,
5441-5451.
|
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E.A.Sieminska,
X.Xu,
A.Savchenko,
and
D.A.Sanders
(2007).
The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 A resolution--a putative transcription factor.
|
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Protein Sci,
16,
543-549.
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PDB code:
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J.W.Lee,
S.Soonsanga,
and
J.D.Helmann
(2007).
A complex thiolate switch regulates the Bacillus subtilis organic peroxide sensor OhrR.
|
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Proc Natl Acad Sci U S A,
104,
8743-8748.
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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.
|
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Mol Cell,
28,
652-664.
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PDB codes:
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K.Miyazono,
M.Tsujimura,
Y.Kawarabayasi,
and
M.Tanokura
(2007).
Crystal structure of an archaeal homologue of multidrug resistance repressor protein, EmrR, from hyperthermophilic archaea Sulfolobus tokodaii strain 7.
|
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Proteins,
67,
1138-1146.
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PDB code:
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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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S.Soonsanga,
M.Fuangthong,
and
J.D.Helmann
(2007).
Mutational analysis of active site residues essential for sensing of organic hydroperoxides by Bacillus subtilis OhrR.
|
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J Bacteriol,
189,
7069-7076.
|
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S.Töwe,
M.Leelakriangsak,
K.Kobayashi,
N.Van Duy,
M.Hecker,
P.Zuber,
and
H.Antelmann
(2007).
The MarR-type repressor MhqR (YkvE) regulates multiple dioxygenases/glyoxalases and an azoreductase which confer resistance to 2-methylhydroquinone and catechol in Bacillus subtilis.
|
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Mol Microbiol,
66,
40-54.
|
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S.Y.Oh,
J.H.Shin,
and
J.H.Roe
(2007).
Dual role of OhrR as a repressor and an activator in response to organic hydroperoxides in Streptomyces coelicolor.
|
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J Bacteriol,
189,
6284-6292.
|
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V.D.Nguyen,
C.Wolf,
U.Mäder,
M.Lalk,
P.Langer,
U.Lindequist,
M.Hecker,
and
H.Antelmann
(2007).
Transcriptome and proteome analyses in response to 2-methylhydroquinone and 6-brom-2-vinyl-chroman-4-on reveal different degradation systems involved in the catabolism of aromatic compounds in Bacillus subtilis.
|
| |
Proteomics,
7,
1391-1408.
|
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C.Kaito,
D.Morishita,
Y.Matsumoto,
K.Kurokawa,
and
K.Sekimizu
(2006).
Novel DNA binding protein SarZ contributes to virulence in Staphylococcus aureus.
|
| |
Mol Microbiol,
62,
1601-1617.
|
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D.W.Ellison,
and
V.L.Miller
(2006).
Regulation of virulence by members of the MarR/SlyA family.
|
| |
Curr Opin Microbiol,
9,
153-159.
|
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J.I.Kliegman,
S.L.Griner,
J.D.Helmann,
R.G.Brennan,
and
A.Glasfeld
(2006).
Structural basis for the metal-selective activation of the manganese transport regulator of Bacillus subtilis.
|
| |
Biochemistry,
45,
3493-3505.
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PDB codes:
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K.H.Chin,
Z.L.Tu,
J.N.Li,
C.C.Chou,
A.H.Wang,
and
S.H.Chou
(2006).
The crystal structure of XC1739: a putative multiple antibiotic-resistance repressor (MarR) from Xanthomonas campestris at 1.8 A resolution.
|
| |
Proteins,
65,
239-242.
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PDB code:
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P.R.Chen,
T.Bae,
W.A.Williams,
E.M.Duguid,
P.A.Rice,
O.Schneewind,
and
C.He
(2006).
An oxidation-sensing mechanism is used by the global regulator MgrA in Staphylococcus aureus.
|
| |
Nat Chem Biol,
2,
591-595.
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PDB code:
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R.P.Saha,
and
P.Chakrabarti
(2006).
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU.
|
| |
BMC Struct Biol,
6,
24.
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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
