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Transcription/DNA
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PDB id
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1cgp
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* Residue conservation analysis
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Gene Ontology (GO) functional annotation
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Cellular component
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intracellular
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1 term
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Biological process
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regulation of transcription
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3 terms
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Biochemical function
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nucleotide binding
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7 terms
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DOI no:
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Science
253:1001-1007
(1991)
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PubMed id:
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Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees.
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S.C.Schultz,
G.C.Shields,
T.A.Steitz.
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ABSTRACT
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The 3 angstrom resolution crystal structure of the Escherichia coli catabolite
gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows
that the DNA is bent by 90 degrees. This bend results almost entirely from two
40 degrees kinks that occur between TG/CA base pairs at positions 5 and 6 on
each side of the dyad axis of the complex. DNA sequence discrimination by CAP
derives both from sequence-dependent distortion of the DNA helix and from direct
hydrogen-bonding interactions between three protein side chains and the exposed
edges of three base pairs in the major groove of the DNA. The structure of this
transcription factor--DNA complex provides insights into possible mechanisms of
transcription activation.
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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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|
|
A.P.Zhang,
Y.Z.Pigli,
and
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Structure of the LexA-DNA complex and implications for SOS box measurement.
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| |
Nature, 466,
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B.Chen,
Y.Xiao,
C.Liu,
C.Li,
and
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(2010).
DNA linking number change induced by sequence-specific DNA-binding proteins.
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| |
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E.L.Fuchs,
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and
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The Pseudomonas aeruginosa Vfr regulator controls global virulence factor expression through cyclic AMP-dependent and -independent mechanisms.
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J Bacteriol, 192,
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Crystal structure of the transcriptional repressor PagR of Bacillus anthracis.
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| |
Microbiology, 156,
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Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH.
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J.P.Peters,
and
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DNA curvature and flexibility in vitro and in vivo.
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| |
Q Rev Biophys, 43,
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J.R.Wickstrum,
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and
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The AraC/XylS family activator RhaS negatively autoregulates rhaSR expression by preventing cyclic AMP receptor protein activation.
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| |
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M.X.Zhao,
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C.C.Zhang,
and
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(2010).
Structural basis for the allosteric control of the global transcription factor NtcA by the nitrogen starvation signal 2-oxoglutarate.
|
| |
Proc Natl Acad Sci U S A, 107,
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|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
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Origins of specificity in protein-DNA recognition.
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| |
Annu Rev Biochem, 79,
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T.Yamashita
(2010).
[Recent studies on gas sensors, CooA, FixL, and Dos]
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| |
Yakugaku Zasshi, 130,
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|
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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.
|
| |
Proc Natl Acad Sci U S A, 106,
4659-4664.
|
|
|
|
|
|
|
A.J.Lee,
R.W.Clark,
H.Youn,
S.Ponter,
and
J.N.Burstyn
(2009).
Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA.
|
| |
Biochemistry, 48,
6585-6597.
|
|
|
|
|
|
|
A.Vindigni,
and
I.D.Hickson
(2009).
RecQ helicases: multiple structures for multiple functions?
|
| |
HFSP J, 3,
153-164.
|
|
|
|
|
|
|
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.
|
| |
Proc Natl Acad Sci U S A, 106,
19830-19835.
|
|
|
PDB code:
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|
|
E.F.Koslover,
and
A.J.Spakowitz
(2009).
Twist- and tension-mediated elastic coupling between DNA-binding proteins.
|
| |
Phys Rev Lett, 102,
178102.
|
|
|
|
|
|
|
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.
|
| |
Proteins, 77,
174-180.
|
|
|
PDB code:
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|
|
H.S.Lee,
R.D.Dimla,
and
P.G.Schultz
(2009).
Protein-DNA photo-crosslinking with a genetically encoded benzophenone-containing amino acid.
|
| |
Bioorg Med Chem Lett, 19,
5222-5224.
|
|
|
|
|
|
|
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.
|
| |
Proc Natl Acad Sci U S A, 106,
16604-16609.
|
|
|
PDB codes:
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|
K.Gurova
(2009).
New hopes from old drugs: revisiting DNA-binding small molecules as anticancer agents.
|
| |
Future Oncol, 5,
1685-1704.
|
|
|
|
|
|
|
M.Xu,
and
Z.Su
(2009).
Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes.
|
| |
BMC Genomics, 10,
23.
|
|
|
|
|
|
|
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.
|
| |
Proc Natl Acad Sci U S A, 106,
6927-6932.
|
|
|
PDB code:
|
|
|
|
|
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|
|
P.L.Privalov,
A.I.Dragan,
and
C.Crane-Robinson
(2009).
The cost of DNA bending.
|
| |
Trends Biochem Sci, 34,
464-470.
|
|
|
|
|
|
|
R.D.Shereda,
N.J.Reiter,
S.E.Butcher,
and
J.L.Keck
(2009).
Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus.
|
| |
J Mol Biol, 386,
612-625.
|
|
|
|
|
|
|
S.R.Tzeng,
and
C.G.Kalodimos
(2009).
Dynamic activation of an allosteric regulatory protein.
|
| |
Nature, 462,
368-372.
|
|
|
|
|
|
|
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.
|
| |
Nucleic Acids Res, 37,
4723-4735.
|
|
|
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.
|
| |
Mol Microbiol, 73,
32-42.
|
|
|
|
|
|
|
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.
|
| |
Microbiology, 154,
1998-2007.
|
|
|
|
|
|
|
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.
|
| |
Infect Immun, 76,
2227-2234.
|
|
|
|
|
|
|
D.Svozil,
J.Kalina,
M.Omelka,
and
B.Schneider
(2008).
DNA conformations and their sequence preferences.
|
| |
Nucleic Acids Res, 36,
3690-3706.
|
|
|
|
|
|
|
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.
|
| |
J Bacteriol, 190,
7584-7590.
|
|
|
|
|
|
|
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.
|
| |
J Bacteriol, 190,
4532-4540.
|
|
|
|
|
|
|
I.Lozada-Chávez,
V.E.Angarica,
J.Collado-Vides,
and
B.Contreras-Moreira
(2008).
The role of DNA-binding specificity in the evolution of bacterial regulatory networks.
|
| |
J Mol Biol, 379,
627-643.
|
|
|
|
|
|
|
M.Gao,
and
J.Skolnick
(2008).
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.
|
| |
Nucleic Acids Res, 36,
3978-3992.
|
|
|
|
|
|
|
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.
|
| |
Nucleic Acids Res, 36,
4797-4807.
|
|
|
|
|
|
|
S.R.Coffin,
and
N.O.Reich
(2008).
Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences.
|
| |
J Biol Chem, 283,
20106-20116.
|
|
|
|
|
|
|
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.
|
| |
BMC Bioinformatics, 9,
436.
|
|
|
|
|
|
|
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.
|
| |
Nat Protoc, 3,
1213-1227.
|
|
|
|
|
|
|
Y.Agari,
A.Kashihara,
S.Yokoyama,
S.Kuramitsu,
and
A.Shinkai
(2008).
Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator.
|
| |
Mol Microbiol, 70,
60-75.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.Akhter,
S.Yellaboina,
A.Farhana,
A.Ranjan,
N.Ahmed,
and
S.E.Hasnain
(2008).
Genome scale portrait of cAMP-receptor protein (CRP) regulons in mycobacteria points to their role in pathogenesis.
|
| |
Gene, 407,
148-158.
|
|
|
|
|
|
|
Y.Shao,
L.S.Feldman-Cohen,
and
R.Osuna
(2008).
Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site.
|
| |
J Mol Biol, 380,
327-339.
|
|
|
|
|
|
|
Y.Tutar
(2008).
Chemical Linkage at Allosteric Activation of E. coli cAMP Receptor Protein.
|
| |
Protein J, 27,
21-29.
|
|
|
|
|
|
|
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.
|
| |
Cell Biochem Funct, 26,
399-405.
|
|
|
|
|
|
|
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.
|
| |
PLoS ONE, 3,
e1450.
|
|
|
|
|
|
|
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.
|
| |
J Biol Inorg Chem, 12,
279-292.
|
|
|
|
|
|
|
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.
|
| |
J Bacteriol, 189,
3891-3901.
|
|
|
|
|
|
|
A.T.Macias,
N.K.Banavali,
and
A.D.MacKerell
(2007).
DNA bending induced by carbocyclic sugar analogs constrained to the north conformation.
|
| |
Biopolymers, 85,
438-449.
|
|
|
|
|
|
|
D.F.Stickle,
and
M.G.Fried
(2007).
Cation binding linked to a sequence-specific CAP-DNA interaction.
|
| |
Biophys Chem, 126,
106-116.
|
|
|
|
|
|
|
F.Spyrakis,
P.Cozzini,
C.Bertoli,
A.Marabotti,
G.E.Kellogg,
and
A.Mozzarelli
(2007).
Energetics of the protein-DNA-water interaction.
|
| |
BMC Struct Biol, 7,
4.
|
|
|
|
|
|
|
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.
|
| |
PLoS ONE, 2,
e301.
|
|
|
PDB code:
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|
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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.
|
| |
Proc Natl Acad Sci U S A, 104,
2092-2097.
|
|
|
|
|
|
|
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.
|
| |
J Bacteriol, 189,
5976-5986.
|
|
|
|
|
|
|
J.Xiong,
C.E.Bauer,
and
A.Pancholy
(2007).
Insight into the haem d1 biosynthesis pathway in heliobacteria through bioinformatics analysis.
|
| |
Microbiology, 153,
3548-3562.
|
|
|
|
|
|
|
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.
|
| |
Nucleic Acids Res, 35,
5073-5084.
|
|
|
PDB codes:
|
|
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|
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|
|
|
L.Saiz,
and
J.M.Vilar
(2007).
Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes.
|
| |
PLoS ONE, 2,
e355.
|
|
|
|
|
|
|
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.
|
| |
Acta Crystallogr D Biol Crystallogr, 63,
282-287.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
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.
|
| |
Nucleic Acids Res, 35,
6611-6624.
|
|
|
|
|
|
|
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.
|
| |
J Mol Biol, 357,
173-183.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.D.Cameron,
and
R.J.Redfield
(2006).
Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria.
|
| |
Nucleic Acids Res, 34,
6001-6014.
|
|
|
|
|
|
|
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.
|
| |
Proc Natl Acad Sci U S A, 103,
13676-13681.
|
|
|
PDB codes:
|
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|
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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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
H.Reents,
I.Gruner,
U.Harmening,
L.H.Böttger,
G.Layer,
P.Heathcote,
A.X.Trautwein,
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E.T.Kool
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Mol Microbiol, 39,
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Structural basis of the redox switch in the OxyR transcription factor.
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Cell, 105,
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PDB codes:
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J.G.Harman
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Allosteric regulation of the cAMP receptor protein.
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Biochim Biophys Acta, 1547,
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J.L.Beck,
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DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli.
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Nucleic Acids Res, 29,
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Proc Natl Acad Sci U S A, 98,
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PDB code:
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M.K.Chan
(2001).
Recent advances in heme-protein sensors.
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Curr Opin Chem Biol, 5,
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N.J.Weyand,
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The essential role of the promoter-proximal subunit of CAP in pap phase variation: Lrp- and helical phase-dependent activation of papBA transcription by CAP from -215.
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Mol Microbiol, 39,
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Chem Biol, 8,
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R.C.Langdon,
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A chimeric activator of transcription that uses two DNA-binding domains to make simultaneous contact with pairs of recognition sites.
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Mol Microbiol, 41,
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R.Fishman,
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Acta Crystallogr D Biol Crystallogr, 57,
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PDB code:
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S.A.Williams,
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(2001).
SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site.
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Nucleic Acids Res, 29,
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Crystal structure of the SarR protein from Staphylococcus aureus.
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Proc Natl Acad Sci U S A, 98,
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PDB code:
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Y.Tanaka,
O.Nureki,
H.Kurumizaka,
S.Fukai,
S.Kawaguchi,
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Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
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EMBO J, 20,
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PDB code:
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A.Maghnouj,
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Regulation of anaerobic arginine catabolism in Bacillus licheniformis by a protein of the Crp/Fnr family.
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FEMS Microbiol Lett, 191,
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A.N.Naimushin,
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Dynamic bending rigidity of a 200-bp DNA in 4 mM ionic strength: a transient polarization grating study.
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Biophys J, 78,
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D.C.Kombo,
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One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein.
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Biopolymers, 53,
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D.J.Lee,
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Analysis of interactions between Activating Region 1 of Escherichia coli FNR protein and the C-terminal domain of the RNA polymerase alpha subunit: use of alanine scanning and suppression genetics.
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Mol Microbiol, 37,
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D.M.van Aalten,
C.C.DiRusso,
J.Knudsen,
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Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold.
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EMBO J, 19,
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PDB code:
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D.S.Daniels,
C.D.Mol,
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S.Kanugula,
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Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding.
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EMBO J, 19,
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PDB codes:
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E.Richet
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EMBO J, 19,
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A study of the CopF repressor of plasmid pAMbeta1 by phage display.
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J Bacteriol, 182,
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F.Colland,
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sigma factor selectivity of Escherichia coli RNA polymerase: role for CRP, IHF and lrp transcription factors.
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EMBO J, 19,
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H.L.Ng,
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The structure of a stable intermediate in the A <--> B DNA helix transition.
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Proc Natl Acad Sci U S A, 97,
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PDB code:
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H.S.Won,
T.Yamazaki,
T.W.Lee,
M.K.Yoon,
S.H.Park,
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Structural understanding of the allosteric conformational change of cyclic AMP receptor protein by cyclic AMP binding.
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Biochemistry, 39,
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J.E.Wibley,
A.E.Pegg,
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Crystal structure of the human O(6)-alkylguanine-DNA alkyltransferase.
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Nucleic Acids Res, 28,
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PDB code:
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K.Röttgers,
N.M.Krohn,
J.Lichota,
C.Stemmer,
T.Merkle,
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DNA-interactions and nuclear localisation of the chromosomal HMG domain protein SSRP1 from maize.
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Plant J, 23,
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L.D.Williams,
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Electrostatic mechanisms of DNA deformation.
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Annu Rev Biophys Biomol Struct, 29,
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Structural and thermodynamic strategies for site-specific DNA binding proteins.
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Structure, 8,
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Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds.
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Biophys J, 78,
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Determining the DNA bending angle induced by non-specific high mobility group-1 (HMG-1) proteins: a novel method.
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Biochemistry, 39,
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M.Lu,
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Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
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Proc Natl Acad Sci U S A, 97,
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PDB code:
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M.Okuda,
Y.Watanabe,
H.Okamura,
F.Hanaoka,
Y.Ohkuma,
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Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface.
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EMBO J, 19,
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PDB codes:
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N.M.Luscombe,
S.E.Austin,
H.M.Berman,
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An overview of the structures of protein-DNA complexes.
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Genome Biol, 1,
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N.Naryshkin,
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V.Mekler,
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Structural organization of the RNA polymerase-promoter open complex.
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Cell, 101,
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P.E.Verdemato,
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F.Zuccotto,
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DNA-binding mechanism of the Escherichia coli Ada O(6)-alkylguanine-DNA alkyltransferase.
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Nucleic Acids Res, 28,
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Q.Huai,
J.D.Colandene,
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M.D.Topal,
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Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
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EMBO J, 19,
3110-3118.
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PDB code:
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W.K.Olson,
and
V.B.Zhurkin
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Modeling DNA deformations.
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Curr Opin Struct Biol, 10,
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W.Meng,
N.J.Savery,
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The Escherichia coli RNA polymerase alpha subunit linker: length requirements for transcription activation at CRP-dependent promoters.
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EMBO J, 19,
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X.Zheng,
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Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR.
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Proc Natl Acad Sci U S A, 97,
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Y.Shi,
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Intersubunit association induces unique allosteric dependence of the T127L CRP mutant on pH.
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Biochemistry, 39,
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DNA bending and wrapping around RNA polymerase: a "revolutionary" model describing transcriptional mechanisms.
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Microbiol Mol Biol Rev, 63,
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C.Place,
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Studies of contacts between T7 RNA polymerase and its promoter reveal features in common with multisubunit RNA polymerases.
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Biochemistry, 38,
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C.Sissi,
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K.Depew,
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Interaction of calicheamicin gamma1(I) and its related carbohydrates with DNA-protein complexes.
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Proc Natl Acad Sci U S A, 96,
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H.G.Griffin,
C.A.Shearman,
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J.Green,
M.J.Gasson,
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Two operons that encode FNR-like proteins in Lactococcus lactis.
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Mol Microbiol, 31,
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D.R.Hall,
D.G.Gourley,
G.A.Leonard,
E.M.Duke,
L.A.Anderson,
D.H.Boxer,
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The high-resolution crystal structure of the molybdate-dependent transcriptional regulator (ModE) from Escherichia coli: a novel combination of domain folds.
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EMBO J, 18,
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PDB codes:
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H.Komori,
F.Matsunaga,
Y.Higuchi,
M.Ishiai,
C.Wada,
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Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution.
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EMBO J, 18,
4597-4607.
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PDB code:
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H.Kono,
and
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Structure-based prediction of DNA target sites by regulatory proteins.
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Proteins, 35,
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I.Muiznieks,
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Efficient control of raf gene expression by CAP and two Raf repressors that bend DNA in opposite directions.
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Biol Chem, 380,
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J.S.Hwang,
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Specific contacts between residues in the DNA-binding domain of the TyrR protein and bases in the operator of the tyrP gene of Escherichia coli.
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J Bacteriol, 181,
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K.L.Meibom,
L.Søgaard-Andersen,
A.S.Mironov,
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Dissection of a surface-exposed portion of the cAMP-CRP complex that mediates transcription activation and repression.
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Mol Microbiol, 32,
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K.Nadassy,
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Structural features of protein-nucleic acid recognition sites.
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Biochemistry, 38,
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L.Landis,
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The cAMP receptor protein CRP can function as an osmoregulator of transcription in Escherichia coli.
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Genes Dev, 13,
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M.D.Nichols,
K.DeAngelis,
J.L.Keck,
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Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11.
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| |
EMBO J, 18,
6177-6188.
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PDB code:
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M.Schade,
C.J.Turner,
K.Lowenhaupt,
A.Rich,
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EMBO J, 18,
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M.Schade,
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The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA.
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| |
Proc Natl Acad Sci U S A, 96,
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PDB code:
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|
N.Baichoo,
and
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Mapping cyclic nucleotide-induced conformational changes in cyclicAMP receptor protein by a protein footprinting technique using different chemical proteases.
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Protein Sci, 8,
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Q.M.Eastman,
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Detection of RAG protein-V(D)J recombination signal interactions near the site of DNA cleavage by UV cross-linking.
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Mol Cell Biol, 19,
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R.Gurlie,
T.H.Duong,
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The role of DNA-protein salt bridges in molecular recognition: a model study.
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Biopolymers, 49,
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R.P.Ojha,
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M.H.Sarma,
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DNA bending and sequence-dependent backbone conformation NMR and computer experiments.
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Eur J Biochem, 265,
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S.G.Smith,
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Functional analysis of the FimE integrase of Escherichia coli K-12: isolation of mutant derivatives with altered DNA inversion preferences.
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Mol Microbiol, 34,
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T.I.Wood,
K.L.Griffith,
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K.W.Jair,
T.D.Schneider,
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Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters.
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Mol Microbiol, 34,
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T.Mahmoudi,
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Addition of positively charged tripeptide to N-terminus of the Fos basic region leucine zipper domain: implications on DNA bending, affinity, and specificity.
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Biopolymers, 50,
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W.S.Tzou,
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Modeling helix-turn-helix protein-induced DNA bending with knowledge-based distance restraints.
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Biophys J, 77,
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Y.Fujii,
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Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences.
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| |
EMBO J, 18,
5028-5041.
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PDB code:
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A.K.Aggarwal,
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