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Transcription/DNA
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PDB id
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1par
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Gene Ontology (GO) functional annotation
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Biological process
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regulation of transcription
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2 terms
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Biochemical function
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DNA binding
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1 term
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DOI no:
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Nature
367:754-757
(1994)
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PubMed id:
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DNA recognition by beta-sheets in the Arc repressor-operator crystal structure.
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B.E.Raumann,
M.A.Rould,
C.O.Pabo,
R.T.Sauer.
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ABSTRACT
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Transcription of the ant gene during lytic growth of bacteriophage P22 (ref. 1)
is regulated by the cooperative binding of two Arc repressor dimers to a
21-base-pair operator site. Here we report the co-crystal structure of this Arc
tetramer-operator complex at 2.6 A resolution. As expected from genetic and
structural studies and from the co-crystal structure of the homologous
Escherichia coli MetJ repressor, each Arc dimer uses an antiparallel beta-sheet
to recognize bases in the major groove. However, the Arc and MetJ complexes
differ in several important ways: the beta-sheet-DNA interactions of Arc are far
less symmetrical; DNA binding by Arc is accompanied by important conformational
changes in the beta-sheet; and Arc uses a different part of its protein surface
for dimer-dimer interactions.
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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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|
|
|
L.Huang,
P.Yin,
X.Zhu,
Y.Zhang,
and
K.Ye
(2011).
Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100.
|
| |
Nucleic Acids Res, 39,
2954-2968.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.Chopra,
S.Agarwal,
S.Verma,
S.Bhatnagar,
and
R.Bhatnagar
(2011).
Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function.
|
| |
J Comput Aided Mol Des, 25,
275-291.
|
|
|
|
|
|
|
E.Diago-Navarro,
A.M.Hernandez-Arriaga,
J.López-Villarejo,
A.J.Muñoz-Gómez,
M.B.Kamphuis,
R.Boelens,
M.Lemonnier,
and
R.Díaz-Orejas
(2010).
parD toxin-antitoxin system of plasmid R1--basic contributions, biotechnological applications and relationships with closely-related toxin-antitoxin systems.
|
| |
FEBS J, 277,
3097-3117.
|
|
|
|
|
|
|
M.van Dijk,
and
A.M.Bonvin
(2010).
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
|
| |
Nucleic Acids Res, 38,
5634-5647.
|
|
|
|
|
|
|
R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
|
| |
Annu Rev Biochem, 79,
233-269.
|
|
|
|
|
|
|
S.Campagne,
O.Saurel,
V.Gervais,
and
A.Milon
(2010).
Structural determinants of specific DNA-recognition by the THAP zinc finger.
|
| |
Nucleic Acids Res, 38,
3466-3476.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.M.Hernández-Arriaga,
T.S.Rubio-Lepe,
M.Espinosa,
and
G.del Solar
(2009).
Repressor CopG prevents access of RNA polymerase to promoter and actively dissociates open complexes.
|
| |
Nucleic Acids Res, 37,
4799-4811.
|
|
|
|
|
|
|
A.Marcovitz,
and
Y.Levy
(2009).
Arc-repressor dimerization on DNA: folding rate enhancement by colocalization.
|
| |
Biophys J, 96,
4212-4220.
|
|
|
|
|
|
|
A.Varsaki,
G.Moncalián,
M.d.e.l. .P.Garcillán-Barcia,
C.Drainas,
and
F.de la Cruz
(2009).
Analysis of ColE1 MbeC unveils an extended ribbon-helix-helix family of nicking accessory proteins.
|
| |
J Bacteriol, 191,
1446-1455.
|
|
|
|
|
|
|
J.Lu,
A.den Dulk-Ras,
P.J.Hooykaas,
and
J.N.Glover
(2009).
Agrobacterium tumefaciens VirC2 enhances T-DNA transfer and virulence through its C-terminal ribbon-helix-helix DNA-binding fold.
|
| |
Proc Natl Acad Sci U S A, 106,
9643-9648.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.Ni,
S.O.Jensen,
N.Ky Tonthat,
T.Berg,
S.M.Kwong,
F.H.Guan,
M.H.Brown,
R.A.Skurray,
N.Firth,
and
M.A.Schumacher
(2009).
The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes.
|
| |
Nucleic Acids Res, 37,
6970-6983.
|
|
|
PDB code:
|
|
|
|
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|
|
M.Overgaard,
J.Borch,
and
K.Gerdes
(2009).
RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB.
|
| |
J Mol Biol, 394,
183-196.
|
|
|
|
|
|
|
M.Zampini,
A.Derome,
S.E.Bailey,
D.Barillà,
and
F.Hayes
(2009).
Recruitment of the ParG segregation protein to different affinity DNA sites.
|
| |
J Bacteriol, 191,
3832-3841.
|
|
|
|
|
|
|
S.Halouska,
Y.Zhou,
D.F.Becker,
and
R.Powers
(2009).
Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex.
|
| |
Proteins, 75,
12-27.
|
|
|
PDB codes:
|
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|
|
Z.Ma,
F.E.Jacobsen,
and
D.P.Giedroc
(2009).
Coordination chemistry of bacterial metal transport and sensing.
|
| |
Chem Rev, 109,
4644-4681.
|
|
|
|
|
|
|
B.N.Borin,
and
A.M.Krezel
(2008).
Structure of HP0564 from Helicobacter pylori identifies it as a new transcriptional regulator.
|
| |
Proteins, 73,
265-268.
|
|
|
PDB code:
|
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|
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I.E.Sánchez,
M.Dellarole,
K.Gaston,
and
G.de Prat Gay
(2008).
Comprehensive comparison of the interaction of the E2 master regulator with its cognate target DNA sites in 73 human papillomavirus types by sequence statistics.
|
| |
Nucleic Acids Res, 36,
756-769.
|
|
|
|
|
|
|
M.J.Bradley,
P.T.Chivers,
and
N.A.Baker
(2008).
Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways.
|
| |
J Mol Biol, 378,
1155-1173.
|
|
|
|
|
|
|
P.Poulain,
A.Saladin,
B.Hartmann,
and
C.Prévost
(2008).
Insights on protein-DNA recognition by coarse grain modelling.
|
| |
J Comput Chem, 29,
2582-2592.
|
|
|
|
|
|
|
S.P.Haugen,
W.Ross,
M.Manrique,
and
R.L.Gourse
(2008).
Fine structure of the promoter-sigma region 1.2 interaction.
|
| |
Proc Natl Acad Sci U S A, 105,
3292-3297.
|
|
|
|
|
|
|
Y.Zhou,
J.D.Larson,
C.A.Bottoms,
E.C.Arturo,
M.T.Henzl,
J.L.Jenkins,
J.C.Nix,
D.F.Becker,
and
J.J.Tanner
(2008).
Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA.
|
| |
J Mol Biol, 381,
174-188.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.L.Benanti,
and
P.T.Chivers
(2007).
The N-terminal arm of the Helicobacter pylori Ni2+-dependent transcription factor NikR is required for specific DNA binding.
|
| |
J Biol Chem, 282,
20365-20375.
|
|
|
|
|
|
|
E.R.Schreiter,
and
C.L.Drennan
(2007).
Ribbon-helix-helix transcription factors: variations on a theme.
|
| |
Nat Rev Microbiol, 5,
710-720.
|
|
|
|
|
|
|
J.Møller-Jensen,
S.Ringgaard,
C.P.Mercogliano,
K.Gerdes,
and
J.Löwe
(2007).
Structural analysis of the ParR/parC plasmid partition complex.
|
| |
EMBO J, 26,
4413-4422.
|
|
|
PDB code:
|
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|
|
|
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|
|
M.A.Schumacher,
T.C.Glover,
A.J.Brzoska,
S.O.Jensen,
T.D.Dunham,
R.A.Skurray,
and
N.Firth
(2007).
Segrosome structure revealed by a complex of ParR with centromere DNA.
|
| |
Nature, 450,
1268-1271.
|
|
|
PDB code:
|
|
|
|
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|
|
M.Oberer,
K.Zangger,
K.Gruber,
and
W.Keller
(2007).
The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.
|
| |
Protein Sci, 16,
1676-1688.
|
|
|
PDB code:
|
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|
|
|
|
|
S.Ringgaard,
J.Löwe,
and
K.Gerdes
(2007).
Centromere pairing by a plasmid-encoded type I ParB protein.
|
| |
J Biol Chem, 282,
28216-28225.
|
|
|
|
|
|
|
D.Prangishvili,
R.A.Garrett,
and
E.V.Koonin
(2006).
Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life.
|
| |
Virus Res, 117,
52-67.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
J.D.Larson,
J.L.Jenkins,
J.P.Schuermann,
Y.Zhou,
D.F.Becker,
and
J.J.Tanner
(2006).
Crystal structures of the DNA-binding domain of Escherichia coli proline utilization A flavoprotein and analysis of the role of Lys9 in DNA recognition.
|
| |
Protein Sci, 15,
2630-2641.
|
|
|
PDB codes:
|
|
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|
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|
|
K.Mattison,
J.S.Wilbur,
M.So,
and
R.G.Brennan
(2006).
Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs.
|
| |
J Biol Chem, 281,
37942-37951.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Wang,
T.E.Wales,
and
M.C.Fitzgerald
(2006).
Conserved thermodynamic contributions of backbone hydrogen bonds in a protein fold.
|
| |
Proc Natl Acad Sci U S A, 103,
2600-2604.
|
|
|
|
|
|
|
M.van Dijk,
A.D.van Dijk,
V.Hsu,
R.Boelens,
and
A.M.Bonvin
(2006).
Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility.
|
| |
Nucleic Acids Res, 34,
3317-3325.
|
|
|
|
|
|
|
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.
|
|
|
PDB codes:
|
|
|
|
|
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|
|
A.Popescu,
A.Karpay,
D.A.Israel,
R.M.Peek,
and
A.M.Krezel
(2005).
Helicobacter pylori protein HP0222 belongs to Arc/MetJ family of transcriptional regulators.
|
| |
Proteins, 59,
303-311.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.M.Ramsey,
P.J.Baynham,
and
D.J.Wozniak
(2005).
Binding of Pseudomonas aeruginosa AlgZ to sites upstream of the algZ promoter leads to repression of transcription.
|
| |
J Bacteriol, 187,
4430-4443.
|
|
|
|
|
|
|
E.Carmelo,
D.Barillà,
A.P.Golovanov,
L.Y.Lian,
A.Derome,
and
F.Hayes
(2005).
The unstructured N-terminal tail of ParG modulates assembly of a quaternary nucleoprotein complex in transcription repression.
|
| |
J Biol Chem, 280,
28683-28691.
|
|
|
|
|
|
|
F.D.Ernst,
E.J.Kuipers,
A.Heijens,
R.Sarwari,
J.Stoof,
C.W.Penn,
J.G.Kusters,
and
A.H.van Vliet
(2005).
The nickel-responsive regulator NikR controls activation and repression of gene transcription in Helicobacter pylori.
|
| |
Infect Immun, 73,
7252-7258.
|
|
|
|
|
|
|
G.Ebersbach,
and
K.Gerdes
(2005).
Plasmid segregation mechanisms.
|
| |
Annu Rev Genet, 39,
453-479.
|
|
|
|
|
|
|
J.N.Sarakatsannis,
and
Y.Duan
(2005).
Statistical characterization of salt bridges in proteins.
|
| |
Proteins, 60,
732-739.
|
|
|
|
|
|
|
K.Gerdes,
S.K.Christensen,
and
A.Løbner-Olesen
(2005).
Prokaryotic toxin-antitoxin stress response loci.
|
| |
Nat Rev Microbiol, 3,
371-382.
|
|
|
|
|
|
|
K.Welfle,
F.Pratto,
R.Misselwitz,
J.Behlke,
J.C.Alonso,
and
H.Welfle
(2005).
Role of the N-terminal region and of beta-sheet residue Thr29 on the activity of the omega2 global regulator from the broad-host range Streptococcus pyogenes plasmid pSM19035.
|
| |
Biol Chem, 386,
881-894.
|
|
|
|
|
|
|
R.K.Tabtiang,
B.O.Cezairliyan,
R.A.Grant,
J.C.Cochrane,
and
R.T.Sauer
(2005).
Consolidating critical binding determinants by noncyclic rearrangement of protein secondary structure.
|
| |
Proc Natl Acad Sci U S A, 102,
2305-2309.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.A.Anderson,
M.H.Cordes,
and
R.T.Sauer
(2005).
Sequence determinants of a conformational switch in a protein structure.
|
| |
Proc Natl Acad Sci U S A, 102,
18344-18349.
|
|
|
|
|
|
|
X.Zhao,
and
R.D.Magnuson
(2005).
Percolation of the phd repressor-operator interface.
|
| |
J Bacteriol, 187,
1901-1912.
|
|
|
|
|
|
|
A.B.de la Hoz,
F.Pratto,
R.Misselwitz,
C.Speck,
W.Weihofen,
K.Welfle,
W.Saenger,
H.Welfle,
and
J.C.Alonso
(2004).
Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats.
|
| |
Nucleic Acids Res, 32,
3136-3147.
|
|
|
|
|
|
|
D.Gu,
Y.Zhou,
V.Kallhoff,
B.Baban,
J.J.Tanner,
and
D.F.Becker
(2004).
Identification and characterization of the DNA-binding domain of the multifunctional PutA flavoenzyme.
|
| |
J Biol Chem, 279,
31171-31176.
|
|
|
|
|
|
|
T.K.Man,
J.S.Yang,
and
G.D.Stormo
(2004).
Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor.
|
| |
Nucleic Acids Res, 32,
4026-4032.
|
|
|
|
|
|
|
A.Guasch,
M.Lucas,
G.Moncalián,
M.Cabezas,
R.Pérez-Luque,
F.X.Gomis-Rüth,
F.de la Cruz,
and
M.Coll
(2003).
Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC.
|
| |
Nat Struct Biol, 10,
1002-1010.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.P.Golovanov,
D.Barillà,
M.Golovanova,
F.Hayes,
and
L.Y.Lian
(2003).
ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon-helix-helix structure.
|
| |
Mol Microbiol, 50,
1141-1153.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.J.Wozniak,
A.B.Sprinkle,
and
P.J.Baynham
(2003).
Control of Pseudomonas aeruginosa algZ expression by the alternative sigma factor AlgT.
|
| |
J Bacteriol, 185,
7297-7300.
|
|
|
|
|
|
|
E.R.Schreiter,
M.D.Sintchak,
Y.Guo,
P.T.Chivers,
R.T.Sauer,
and
C.L.Drennan
(2003).
Crystal structure of the nickel-responsive transcription factor NikR.
|
| |
Nat Struct Biol, 10,
794-799.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.Ma,
and
M.C.Fitzgerald
(2003).
A new H/D exchange- and mass spectrometry-based method for thermodynamic analysis of protein-DNA interactions.
|
| |
Chem Biol, 10,
1205-1213.
|
|
|
|
|
|
|
S.B.Mulrooney,
and
R.P.Hausinger
(2003).
Nickel uptake and utilization by microorganisms.
|
| |
FEMS Microbiol Rev, 27,
239-261.
|
|
|
|
|
|
|
S.X.Cohen,
M.Moulin,
S.Hashemolhosseini,
K.Kilian,
M.Wegner,
and
C.W.Müller
(2003).
Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition.
|
| |
EMBO J, 22,
1835-1845.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
F.S.Silbaq,
S.E.Ruttenberg,
and
G.D.Stormo
(2002).
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections.
|
| |
Nucleic Acids Res, 30,
5539-5548.
|
|
|
|
|
|
|
G.del Solar,
A.M.Hernández-Arriaga,
F.X.Gomis-Rüth,
M.Coll,
and
M.Espinosa
(2002).
A genetically economical family of plasmid-encoded transcriptional repressors involved in control of plasmid copy number.
|
| |
J Bacteriol, 184,
4943-4951.
|
|
|
|
|
|
|
L.M.Iyer,
E.V.Koonin,
and
L.Aravind
(2002).
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.
|
| |
Genome Biol, 3,
RESEARCH0012.
|
|
|
|
|
|
|
M.A.Schumacher,
M.C.Miller,
S.Grkovic,
M.H.Brown,
R.A.Skurray,
and
R.G.Brennan
(2002).
Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR.
|
| |
EMBO J, 21,
1210-1218.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.A.Pavlov,
D.I.Cherny,
I.V.Nazimov,
A.I.Slesarev,
and
V.Subramaniam
(2002).
Identification, cloning and characterization of a new DNA-binding protein from the hyperthermophilic methanogen Methanopyrus kandleri.
|
| |
Nucleic Acids Res, 30,
685-694.
|
|
|
|
|
|
|
R.C.Deo,
C.M.Groft,
K.R.Rajashankar,
and
S.K.Burley
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Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer.
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Cell, 108,
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PDB code:
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A.Berggrun,
and
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Contributions of distinct quaternary contacts to cooperative operator binding by Mnt repressor.
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Mol Cell, 8,
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Nucleic Acids Res, 29,
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Proc Natl Acad Sci U S A, 98,
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Solution structure of the DNA-binding domain of TraM.
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| |
Biochemistry, 40,
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PDB code:
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A.K.Srivastava,
and
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(2000).
Evidence for partial secondary structure formation in the transition state for arc repressor refolding and dimerization.
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Biochemistry, 39,
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Structure, 8,
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PDB codes:
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N.M.Luscombe,
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Stability and DNA binding of the phd protein of the phage P1 plasmid addiction system.
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J Biol Chem, 274,
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(1999).
Origins of DNA-binding specificity: role of protein contacts with the DNA backbone.
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Proc Natl Acad Sci U S A, 96,
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PDB codes:
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M.H.Cordes,
and
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(1999).
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Protein Sci, 8,
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Thermodynamic properties and DNA binding of the ParD protein from the broad host-range plasmid RK2/RP4 killing system.
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Biol Chem, 380,
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P.J.Baynham,
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Pseudomonas aeruginosa AlgZ, a ribbon-helix-helix DNA-binding protein, is essential for alginate synthesis and algD transcriptional activation.
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Mol Microbiol, 33,
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P.L.Lum,
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Specific DNA recognition by F Factor TraY involves beta-sheet residues.
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J Biol Chem, 274,
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NikR is a ribbon-helix-helix DNA-binding protein.
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Protein Sci, 8,
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Optimizing the stability of single-chain proteins by linker length and composition mutagenesis.
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Proc Natl Acad Sci U S A, 95,
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C.R.Robinson,
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Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease.
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Proc Natl Acad Sci U S A, 95,
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Amino acid-amino acid contacts at the cooperativity interface of the bacteriophage lambda and P22 repressors.
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Genes Dev, 12,
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F.X.Gomis-Rüth,
M.Solá,
P.Acebo,
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(1998).
The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator.
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| |
EMBO J, 17,
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PDB codes:
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|
J.F.Schildbach,
C.R.Robinson,
and
R.T.Sauer
(1998).
Biophysical characterization of the TraY protein of Escherichia coli F factor.
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| |
J Biol Chem, 273,
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K.Taki,
T.Abo,
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(1998).
Regulatory mechanisms in expression of the traY-I operon of sex factor plasmid R100: involvement of traJ and traY gene products.
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| |
Genes Cells, 3,
331-345.
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M.D.Allen,
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(1998).
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
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| |
EMBO J, 17,
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PDB codes:
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M.K.Shirra,
and
U.Hansen
(1998).
LSF and NTF-1 share a conserved DNA recognition motif yet require different oligomerization states to form a stable protein-DNA complex.
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J Biol Chem, 273,
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M.Newman,
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(1998).
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
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| |
EMBO J, 17,
5466-5476.
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PDB code:
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X.Barril,
C.Alemán,
M.Orozco,
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Salt bridge interactions: stability of the ionic and neutral complexes in the gas phase, in solution, and in proteins.
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Proteins, 32,
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Y.Shi,
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(1998).
Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling.
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| |
Cell, 94,
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PDB code:
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A.H.Lauber,
T.J.Barrett,
M.Subramaniam,
M.Schuchard,
and
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(1997).
A DNA-binding element for a steroid receptor-binding factor is flanked by dual nuclear matrix DNA attachment sites in the c-myc gene promoter.
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J Biol Chem, 272,
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M.A.Kercher,
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Lac repressor-operator complex.
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| |
Curr Opin Struct Biol, 7,
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K.Yamasaki,
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DNA recognition by beta-sheets.
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Biopolymers, 44,
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Nature of DNA binding and RNA polymerase interaction of the Bordetella pertussis BvgA transcriptional activator at the fha promoter.
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J Bacteriol, 179,
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X.Duan,
F.S.Gimble,
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(1997).
Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity.
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| |
Cell, 89,
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|
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PDB code:
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|
C.D.Waldburger,
T.Jonsson,
and
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(1996).
Barriers to protein folding: formation of buried polar interactions is a slow step in acquisition of structure.
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| |
Proc Natl Acad Sci U S A, 93,
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D.Moras,
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Getting into the major groove. Protein-RNA interactions.
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| |
Curr Biol, 6,
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The DegP and DegQ periplasmic endoproteases of Escherichia coli: specificity for cleavage sites and substrate conformation.
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J Bacteriol, 178,
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P.M.Silverman,
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Effect of traY amber mutations on F-plasmid traY promoter activity in vivo.
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J Bacteriol, 178,
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Autoregulation of the plasmid addiction operon of bacteriophage P1.
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J Biol Chem, 271,
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Thermodynamics of sequence-specific protein-DNA interactions.
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Dual regulation of open-complex formation and promoter clearance by Arc explains a novel repressor to activator switch.
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Proc Natl Acad Sci U S A, 93,
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The F plasmid traY gene product binds DNA as a monomer or a dimer: structural and functional implications.
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Dramatic changes in DNA-binding specificity caused by single residue substitutions in an Arc/Mnt hybrid repressor.
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Are buried salt bridges important for protein stability and conformational specificity?
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| |
Nat Struct Biol, 2,
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PDB code:
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|
|
G.Siligardi,
and
A.F.Drake
(1995).
The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides.
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Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.
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Regulation of lrp gene expression by H-NS and Lrp proteins in Escherichia coli: dominant negative mutations in lrp.
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Cold denaturation of a repressor-operator complex: the role of entropy in protein-DNA recognition.
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Proc Natl Acad Sci U S A, 91,
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Protein stability effects of a complete set of alanine substitutions in Arc repressor.
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Nat Struct Biol, 1,
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Structure of PvuII endonuclease with cognate DNA.
|
| |
EMBO J, 13,
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PDB code:
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Citation data come partly from CiteXplore and partly
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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|
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