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.Zhao,
A.Volkov,
V.H.Veldore,
J.A.Hoch,
and
K.I.Varughese
(2010).
Crystal structure of the transcriptional repressor PagR of Bacillus anthracis.
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Microbiology, 156,
385-391.
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A.J.Jervis,
J.C.Crack,
G.White,
P.J.Artymiuk,
M.R.Cheesman,
A.J.Thomson,
N.E.Le Brun,
and
J.Green
(2009).
The O2 sensitivity of the transcription factor FNR is controlled by Ser24 modulating the kinetics of [4Fe-4S] to [2Fe-2S] conversion.
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Proc Natl Acad Sci U S A, 106,
4659-4664.
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A.Vindigni,
and
I.D.Hickson
(2009).
RecQ helicases: multiple structures for multiple functions?
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HFSP J, 3,
153-164.
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B.P.Hudson,
J.Quispe,
S.Lara-González,
Y.Kim,
H.M.Berman,
E.Arnold,
R.H.Ebright,
and
C.L.Lawson
(2009).
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
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Proc Natl Acad Sci U S A, 106,
19830-19835.
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PDB code:
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E.F.Koslover,
and
A.J.Spakowitz
(2009).
Twist- and tension-mediated elastic coupling between DNA-binding proteins.
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Phys Rev Lett, 102,
178102.
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G.Giardina,
S.Rinaldo,
N.Castiglione,
M.Caruso,
and
F.Cutruzzolà
(2009).
A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR.
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Proteins, 77,
174-180.
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PDB code:
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H.Sharma,
S.Yu,
J.Kong,
J.Wang,
and
T.A.Steitz
(2009).
Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.
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Proc Natl Acad Sci U S A, 106,
16604-16609.
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M.Xu,
and
Z.Su
(2009).
Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes.
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BMC Genomics, 10,
23.
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N.Popovych,
S.R.Tzeng,
M.Tonelli,
R.H.Ebright,
and
C.G.Kalodimos
(2009).
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein.
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Proc Natl Acad Sci U S A, 106,
6927-6932.
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PDB code:
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S.R.Tzeng,
and
C.G.Kalodimos
(2009).
Dynamic activation of an allosteric regulatory protein.
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Nature, 462,
368-372.
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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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U.M.Pinto,
and
S.C.Winans
(2009).
Dimerization of the quorum-sensing transcription factor TraR enhances resistance to cytoplasmic proteolysis.
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Mol Microbiol, 73,
32-42.
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C.D.Doern,
R.C.Holder,
and
S.D.Reid
(2008).
Point mutations within the streptococcal regulator of virulence (Srv) alter protein-DNA interactions and Srv function.
|
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Microbiology, 154,
1998-2007.
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D.M.Hunt,
J.W.Saldanha,
J.F.Brennan,
P.Benjamin,
M.Strom,
J.A.Cole,
C.L.Spreadbury,
and
R.S.Buxton
(2008).
Single nucleotide polymorphisms that cause structural changes in the cyclic AMP receptor protein transcriptional regulator of the tuberculosis vaccine strain Mycobacterium bovis BCG alter global gene expression without attenuating growth.
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Infect Immun, 76,
2227-2234.
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D.Svozil,
J.Kalina,
M.Omelka,
and
B.Schneider
(2008).
DNA conformations and their sequence preferences.
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Nucleic Acids Res, 36,
3690-3706.
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E.Olmedo-Verd,
A.Valladares,
E.Flores,
A.Herrero,
and
A.M.Muro-Pastor
(2008).
Role of two NtcA-binding sites in the complex ntcA gene promoter of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120.
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J Bacteriol, 190,
7584-7590.
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H.Youn,
J.Koh,
and
G.P.Roberts
(2008).
Two-state allosteric modeling suggests protein equilibrium as an integral component for cyclic AMP (cAMP) specificity in the cAMP receptor protein of Escherichia coli.
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J Bacteriol, 190,
4532-4540.
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M.Gao,
and
J.Skolnick
(2008).
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.
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Nucleic Acids Res, 36,
3978-3992.
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S.Lindemose,
P.E.Nielsen,
and
N.E.Møllegaard
(2008).
Dissecting direct and indirect readout of cAMP receptor protein DNA binding using an inosine and 2,6-diaminopurine in vitro selection system.
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Nucleic Acids Res, 36,
4797-4807.
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S.R.Coffin,
and
N.O.Reich
(2008).
Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences.
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J Biol Chem, 283,
20106-20116.
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V.E.Angarica,
A.G.Pérez,
A.T.Vasconcelos,
J.Collado-Vides,
and
B.Contreras-Moreira
(2008).
Prediction of TF target sites based on atomistic models of protein-DNA complexes.
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BMC Bioinformatics, 9,
436.
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X.J.Lu,
and
W.K.Olson
(2008).
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
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Nat Protoc, 3,
1213-1227.
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Y.Tutar
(2008).
Chemical Linkage at Allosteric Activation of E. coli cAMP Receptor Protein.
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Protein J, 27,
21-29.
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Y.Tutar
(2008).
Syn, anti, and finally both conformations of cyclic AMP are involved in the CRP-dependent transcription initiation mechanism in E. coli lac operon.
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Cell Biochem Funct, 26,
399-405.
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Z.Xu,
Y.Zhou,
L.Li,
R.Zhou,
S.Xiao,
Y.Wan,
S.Zhang,
K.Wang,
W.Li,
L.Li,
H.Jin,
M.Kang,
B.Dalai,
T.Li,
L.Liu,
Y.Cheng,
L.Zhang,
T.Xu,
H.Zheng,
S.Pu,
B.Wang,
W.Gu,
X.L.Zhang,
G.F.Zhu,
S.Wang,
G.P.Zhao,
and
H.Chen
(2008).
Genome Biology of Actinobacillus pleuropneumoniae JL03, an Isolate of Serotype 3 Prevalent in China.
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PLoS ONE, 3,
e1450.
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A.Myari,
N.Hadjiliadis,
A.Garoufis,
J.Malina,
and
V.Brabec
(2007).
NMR analysis of duplex d(CGCGATCGCG)2 modified by Lambda- and Delta-[Ru(bpy)2(m-GHK)]Cl2 and DNA photocleavage study.
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J Biol Inorg Chem, 12,
279-292.
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A.Shinkai,
S.Kira,
N.Nakagawa,
A.Kashihara,
S.Kuramitsu,
and
S.Yokoyama
(2007).
Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8.
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J Bacteriol, 189,
3891-3901.
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A.T.Macias,
N.K.Banavali,
and
A.D.MacKerell
(2007).
DNA bending induced by carbocyclic sugar analogs constrained to the north conformation.
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Biopolymers, 85,
438-449.
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F.Spyrakis,
P.Cozzini,
C.Bertoli,
A.Marabotti,
G.E.Kellogg,
and
A.Mozzarelli
(2007).
Energetics of the protein-DNA-water interaction.
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BMC Struct Biol, 7,
4.
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I.Laponogov,
D.A.Veselkov,
M.K.Sohi,
X.S.Pan,
A.Achari,
C.Yang,
J.D.Ferrara,
L.M.Fisher,
and
M.R.Sanderson
(2007).
Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target.
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PLoS ONE, 2,
e301.
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PDB code:
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J.C.Crack,
J.Green,
M.R.Cheesman,
N.E.Le Brun,
and
A.J.Thomson
(2007).
Superoxide-mediated amplification of the oxygen-induced switch from [4Fe-4S] to [2Fe-2S] clusters in the transcriptional regulator FNR.
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Proc Natl Acad Sci U S A, 104,
2092-2097.
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J.Makhlin,
T.Kofman,
I.Borovok,
C.Kohler,
S.Engelmann,
G.Cohen,
and
Y.Aharonowitz
(2007).
Staphylococcus aureus ArcR controls expression of the arginine deiminase operon.
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J Bacteriol, 189,
5976-5986.
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K.Yamasaki,
T.Akiba,
T.Yamasaki,
and
K.Harata
(2007).
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.
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Nucleic Acids Res, 35,
5073-5084.
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PDB codes:
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L.Saiz,
and
J.M.Vilar
(2007).
Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes.
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PLoS ONE, 2,
e355.
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M.Borjigin,
H.Li,
N.D.Lanz,
R.L.Kerby,
G.P.Roberts,
and
T.L.Poulos
(2007).
Structure-based hypothesis on the activation of the CO-sensing transcription factor CooA.
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Acta Crystallogr D Biol Crystallogr, 63,
282-287.
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PDB code:
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P.S.Pallan,
P.Lubini,
M.Bolli,
and
M.Egli
(2007).
Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing.
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Nucleic Acids Res, 35,
6611-6624.
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A.A.Napoli,
C.L.Lawson,
R.H.Ebright,
and
H.M.Berman
(2006).
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.
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J Mol Biol, 357,
173-183.
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PDB codes:
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A.D.Cameron,
and
R.J.Redfield
(2006).
Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria.
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| |
Nucleic Acids Res, 34,
6001-6014.
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E.R.Schreiter,
S.C.Wang,
D.B.Zamble,
and
C.L.Drennan
(2006).
NikR-operator complex structure and the mechanism of repressor activation by metal ions.
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Proc Natl Acad Sci U S A, 103,
13676-13681.
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PDB codes:
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G.Han,
C.T.Martin,
and
V.M.Rotello
(2006).
Stability of gold nanoparticle-bound DNA toward biological, physical, and chemical agents.
|
| |
Chem Biol Drug Des, 67,
78-82.
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H.Komori,
K.Satomoto,
Y.Ueda,
N.Shibata,
S.Inagaki,
S.Yoshioka,
S.Aono,
and
Y.Higuchi
(2006).
Crystallization and preliminary X-ray analysis of CooA from Carboxydothermus hydrogenoformans.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun, 62,
471-473.
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H.Reents,
I.Gruner,
U.Harmening,
L.H.Böttger,
G.Layer,
P.Heathcote,
A.X.Trautwein,
D.Jahn,
and
E.Härtig
(2006).
Bacillus subtilis Fnr senses oxygen via a [4Fe-4S] cluster coordinated by three cysteine residues without change in the oligomeric state.
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| |
Mol Microbiol, 60,
1432-1445.
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K.Fukuzawa,
Y.Komeiji,
Y.Mochizuki,
A.Kato,
T.Nakano,
and
S.Tanaka
(2006).
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study.
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| |
J Comput Chem, 27,
948-960.
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K.Gábor,
C.S.Veríssimo,
B.C.Cyran,
P.Ter Horst,
N.P.Meijer,
H.Smidt,
W.M.de Vos,
and
J.van der Oost
(2006).
Characterization of CprK1, a CRP/FNR-type transcriptional regulator of halorespiration from Desulfitobacterium hafniense.
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J Bacteriol, 188,
2604-2613.
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K.Yokoyama,
S.A.Ishijima,
L.Clowney,
H.Koike,
H.Aramaki,
C.Tanaka,
K.Makino,
and
M.Suzuki
(2006).
Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors.
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FEMS Microbiol Rev, 30,
89.
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L.S.Feldman-Cohen,
Y.Shao,
D.Meinhold,
C.Miller,
W.Colón,
and
R.Osuna
(2006).
Common and variable contributions of Fis residues to high-affinity binding at different DNA sequences.
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J Bacteriol, 188,
2081-2095.
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M.Akif,
Y.Akhter,
S.E.Hasnain,
and
S.C.Mande
(2006).
Crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis CRP/FNR family transcription regulator.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 62,
873-875.
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M.Berrera,
S.Pantano,
and
P.Carloni
(2006).
cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations.
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Biophys J, 90,
3428-3433.
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M.J.Wilson,
and
I.L.Lamont
(2006).
Mutational analysis of an extracytoplasmic-function sigma factor to investigate its interactions with RNA polymerase and DNA.
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J Bacteriol, 188,
1935-1942.
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M.P.Killoran,
and
J.L.Keck
(2006).
Sit down, relax and unwind: structural insights into RecQ helicase mechanisms.
|
| |
Nucleic Acids Res, 34,
4098-4105.
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P.Thaw,
S.E.Sedelnikova,
T.Muranova,
S.Wiese,
S.Ayora,
J.C.Alonso,
A.B.Brinkman,
J.Akerboom,
J.van der Oost,
and
J.B.Rafferty
(2006).
Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.
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| |
Nucleic Acids Res, 34,
1439-1449.
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PDB codes:
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R.J.McDonald,
J.D.Kahn,
and
L.J.Maher
(2006).
DNA bending by bHLH charge variants.
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| |
Nucleic Acids Res, 34,
4846-4856.
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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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S.H.Bae,
S.H.Yun,
D.Sun,
H.M.Lim,
and
B.S.Choi
(2006).
Structural and dynamic basis of a supercoiling-responsive DNA element.
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| |
Nucleic Acids Res, 34,
254-261.
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PDB codes:
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W.A.Weihofen,
A.Cicek,
F.Pratto,
J.C.Alonso,
and
W.Saenger
(2006).
Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription.
|
| |
Nucleic Acids Res, 34,
1450-1458.
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PDB codes:
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A.Kanhere,
and
M.Bansal
(2005).
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes.
|
| |
Nucleic Acids Res, 33,
3165-3175.
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A.Sarai,
and
H.Kono
(2005).
Protein-DNA recognition patterns and predictions.
|
| |
Annu Rev Biophys Biomol Struct, 34,
379-398.
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C.A.Davis,
M.W.Capp,
M.T.Record,
and
R.M.Saecker
(2005).
The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase.
|
| |
Proc Natl Acad Sci U S A, 102,
285-290.
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C.H.Reccius,
J.T.Mannion,
J.D.Cross,
and
H.G.Craighead
(2005).
Compression and free expansion of single DNA molecules in nanochannels.
|
| |
Phys Rev Lett, 95,
268101.
|
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D.A.Rodionov,
I.L.Dubchak,
A.P.Arkin,
E.J.Alm,
and
M.S.Gelfand
(2005).
Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.
|
| |
PLoS Comput Biol, 1,
e55.
|
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G.Bai,
L.A.McCue,
and
K.A.McDonough
(2005).
Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein.
|
| |
J Bacteriol, 187,
7795-7804.
|
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H.Youn,
M.V.Thorsteinsson,
M.Conrad,
R.L.Kerby,
and
G.P.Roberts
(2005).
Dual roles of an E-helix residue, Glu167, in the transcriptional activator function of CooA.
|
| |
J Bacteriol, 187,
2573-2581.
|
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J.Benach,
W.C.Edstrom,
I.Lee,
K.Das,
B.Cooper,
R.Xiao,
J.Liu,
B.Rost,
T.B.Acton,
G.T.Montelione,
and
J.F.Hunt
(2005).
The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.
|
| |
Acta Crystallogr D Biol Crystallogr, 61,
589-598.
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PDB code:
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J.Magee,
and
J.Warwicker
(2005).
Simulation of non-specific protein-mRNA interactions.
|
| |
Nucleic Acids Res, 33,
6694-6699.
|
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K.Shi,
C.K.Brown,
Z.Y.Gu,
B.K.Kozlowicz,
G.M.Dunny,
D.H.Ohlendorf,
and
C.A.Earhart
(2005).
Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis.
|
| |
Proc Natl Acad Sci U S A, 102,
18596-18601.
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PDB codes:
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L.Rickman,
C.Scott,
D.M.Hunt,
T.Hutchinson,
M.C.Menéndez,
R.Whalan,
J.Hinds,
M.J.Colston,
J.Green,
and
R.S.Buxton
(2005).
A member of the cAMP receptor protein family of transcription regulators in Mycobacterium tuberculosis is required for virulence in mice and controls transcription of the rpfA gene coding for a resuscitation promoting factor.
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| |
Mol Microbiol, 56,
1274-1286.
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M.Eiting,
G.Hagelüken,
W.D.Schubert,
and
D.W.Heinz
(2005).
The mutation G145S in PrfA, a key virulence regulator of Listeria monocytogenes, increases DNA-binding affinity by stabilizing the HTH motif.
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| |
Mol Microbiol, 56,
433-446.
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PDB codes:
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M.Marilley,
A.Sanchez-Sevilla,
and
J.Rocca-Serra
(2005).
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PDB code:
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Proc Natl Acad Sci U S A, 97,
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PDB code:
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Nucleic Acids Res, 26,
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Proc Natl Acad Sci U S A, 95,
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PDB code:
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PDB codes:
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J.K.Strauss-Soukup,
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Biochemistry, 37,
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Nat Struct Biol, 4,
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PDB code:
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H.S.Subramanya,
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Crystal structure of the site-specific recombinase, XerD.
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EMBO J, 16,
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PDB code:
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J.L.Miller,
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Proc Natl Acad Sci U S A, 94,
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PDB code:
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J.M.Schurr,
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Eur J Biochem, 243,
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Critical base pairs and amino acid residues for protein-DNA interaction between the TyrR protein and tyrP operator of Escherichia coli.
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J Bacteriol, 179,
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Cyclic AMP receptor protein functions as a repressor of the osmotically inducible promoter proP P1 in Escherichia coli.
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J Bacteriol, 179,
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Biochemistry, 36,
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Nat Struct Biol, 4,
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PDB code:
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L.A.Anderson,
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Characterisation of the molybdenum-responsive ModE regulatory protein and its binding to the promoter region of the modABCD (molybdenum transport) operon of Escherichia coli.
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Biopolymers, 44,
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Joining the two domains of a group I ribozyme to form the catalytic core.
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Solution structure of the ATF-2 recognition site and its interaction with the ATF-2 peptide.
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Nucleic Acids Res, 25,
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PDB code:
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M.Sunnerhagen,
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Nat Struct Biol, 4,
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PDB code:
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M.Tateno,
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Mapping conformational changes in a protein: application of a protein footprinting technique to cAMP-induced conformational changes in cAMP receptor protein.
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Biochemistry, 36,
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197 a.a.
