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Contents |
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* Residue conservation analysis
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PDB id:
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Transcription/DNA
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Title:
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Crystal structure of trp repressor operator complex at atomi resolution
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Structure:
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DNA (5'- d( Tp Gp Tp Ap Cp Tp Ap Gp Tp Tp Ap Ap Cp Tp Ap Gp T p Ap C chain: i, j, k, l. Engineered: yes. Protein (trp repressor). Chain: a, c, e, g
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Source:
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Synthetic: yes. Escherichia coli str. K12 substr.. Organism_taxid: 316407. Strain: w3110
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Biol. unit:
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Tetramer (from
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Resolution:
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Authors:
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Z.Otwinowski,R.W.Schevitz,R.-G.Zhang,C.L.Lawson,A.J.Joachimi R.Marmorstein,B.F.Luisi,P.B.Sigler
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Key ref:
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Z.Otwinowski
et al.
(1988).
Crystal structure of trp repressor/operator complex at atomic resolution.
Nature,
335,
321-329.
PubMed id:
DOI:
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Date:
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30-Aug-92
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Release date:
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31-Jan-94
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PROCHECK
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Headers
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References
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Gene Ontology (GO) functional annotation
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Cellular component
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intracellular
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2 terms
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Biological process
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transcription, DNA-dependent
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2 terms
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Biochemical function
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DNA binding
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3 terms
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DOI no:
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Nature
335:321-329
(1988)
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PubMed id:
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Crystal structure of trp repressor/operator complex at atomic resolution.
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Z.Otwinowski,
R.W.Schevitz,
R.G.Zhang,
C.L.Lawson,
A.Joachimiak,
R.Q.Marmorstein,
B.F.Luisi,
P.B.Sigler.
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ABSTRACT
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The crystal structure of the trp repressor/operator complex shows an extensive
contact surface, including 24 direct and 6 solvent-mediated hydrogen bonds to
the phosphate groups of the DNA. There are no direct hydrogen bonds or non-polar
contacts to the bases that can explain the repressor's specificity for the
operator sequence. Rather, the sequence seems to be recognized indirectly
through its effects on the geometry of the phosphate backbone, which in turn
permits the formation of a stable interface. Water-mediated polar contacts to
the bases also appear to contribute part of the specificity.
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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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Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
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Nucleic Acids Res, 39,
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PDB code:
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PDB code:
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Half-Site DNA sequence and spacing length contributions to PrrA binding to PrrA site 2 of RSP3361 in Rhodobacter sphaeroides 2.4.1.
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J Bacteriol, 191,
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and
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Signatures of protein-DNA recognition in free DNA binding sites.
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J Mol Biol, 386,
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PDB codes:
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P.Athri,
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Molecular dynamics of water-mediated interactions of a linear benzimidazole-biphenyl diamidine with the DNA minor groove.
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J Am Chem Soc, 131,
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P.S.Ho
(2009).
Detailed mechanism for transposition by TnpA transposase involves DNA shape rather than direct protein-DNA recognition to generate an active nucleoprotein complex.
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F1000 Biol Rep, 1,
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The role of DNA shape in protein-DNA recognition.
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Nature, 461,
1248-1253.
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T.R.Kahn,
K.K.Fong,
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(2009).
An FTIR investigation of flanking sequence effects on the structure and flexibility of DNA binding sites.
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Biochemistry, 48,
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W.Li,
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and
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Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2.
|
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Proc Natl Acad Sci U S A, 106,
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PDB code:
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A.C.Babic,
E.J.Little,
V.M.Manohar,
J.Bitinaite,
and
N.C.Horton
(2008).
DNA distortion and specificity in a sequence-specific endonuclease.
|
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J Mol Biol, 383,
186-204.
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PDB codes:
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A.Marabotti,
F.Spyrakis,
A.Facchiano,
P.Cozzini,
S.Alberti,
G.E.Kellogg,
and
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(2008).
Energy-based prediction of amino acid-nucleotide base recognition.
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J Comput Chem, 29,
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E.J.Little,
A.C.Babic,
and
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(2008).
Early interrogation and recognition of DNA sequence by indirect readout.
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Structure, 16,
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PDB code:
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G.Cui,
and
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(2008).
The intrinsic dynamics and function of nickel-binding regulatory protein: insights from elastic network analysis.
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J.Messens,
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Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli.
|
| |
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PDB code:
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T.Yamane,
H.Okamura,
M.Ikeguchi,
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and
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|
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L.S.Feldman-Cohen,
and
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(2008).
Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site.
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Energetics of the protein-DNA-water interaction.
|
| |
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and
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Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency.
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| |
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and
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DNA sequence-specific recognition by a transcriptional regulator requires indirect readout of A-tracts.
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Nucleic Acids Res, 35,
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and
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(2007).
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.
|
| |
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PDB codes:
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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,
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PDB codes:
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C.Chen,
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and
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(2006).
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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,
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F.A.Hays,
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and
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Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription.
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PDB codes:
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A.Sarai,
and
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Protein-DNA recognition patterns and predictions.
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PDB codes:
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H.Viadiu,
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(2005).
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A.A.Kornyshev,
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(2004).
E. coli trp repressor forms a domain-swapped array in aqueous alcohol.
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| |
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PDB code:
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F.R.Wibowo,
C.Rauch,
M.Trieb,
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and
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J Biol Chem, 279,
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PDB code:
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Biopolymers, 75,
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and
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(2004).
Shape-selective RNA recognition by cysteinyl-tRNA synthetase.
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| |
Nat Struct Mol Biol, 11,
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PDB code:
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A.M.Ababneh,
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and
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(2003).
Solvation of nucleosides in aqueous mixtures of organic solvents: relevance to DNA open basepairs.
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Comparing the fine specificity of DNA binding by NF-kappaB p50 and p52 using principal coordinates analysis.
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Nucleic Acids Res, 31,
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B.M.Swalla,
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(2003).
Conservation of structure and function among tyrosine recombinases: homology-based modeling of the lambda integrase core-binding domain.
|
| |
Nucleic Acids Res, 31,
805-818.
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PDB code:
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E.M.Panina,
A.G.Vitreschak,
A.A.Mironov,
and
M.S.Gelfand
(2003).
Regulation of biosynthesis and transport of aromatic amino acids in low-GC Gram-positive bacteria.
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(2003).
A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water.
|
| |
Chem Biol, 10,
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PDB codes:
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H.J.Ahn,
H.W.Kim,
H.J.Yoon,
B.I.Lee,
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J.Chai,
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PDB code:
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Structure, 8,
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PDB codes:
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D.C.Kombo,
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PDB code:
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PDB code:
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J Biol Chem, 274,
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PDB code:
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Proc Natl Acad Sci U S A, 96,
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PDB code:
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EMBO J, 18,
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PDB code:
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Biopolymers, 50,
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Major and minor groove contacts in retroviral integrase-LTR interactions.
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Biochemistry, 38,
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Hydration and recognition of methylated CpG steps in DNA.
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EMBO J, 17,
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PDB codes:
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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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Biochemistry, 37,
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Cold Spring Harb Symp Quant Biol, 63,
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Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG).
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Biophys J, 74,
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PDB codes:
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M.A.Schumacher,
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Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.
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EMBO J, 17,
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M.Feig,
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Crystallographic water sites from a theoretical perspective.
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Structure, 6,
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Study of a noncovalent trp repressor: DNA operator complex by electrospray ionization time-of-flight mass spectrometry.
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Protein Sci, 7,
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Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity.
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Protein Sci, 7,
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Nucleic Acids Res, 26,
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Mutational analysis of the NH2-terminal arms of the trp repressor indicates a multifunctional domain.
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Mol Microbiol, 27,
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New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB.
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How glutaminyl-tRNA synthetase selects glutamine.
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Structure, 6,
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PDB code:
|
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W.K.Olson,
A.A.Gorin,
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Proc Natl Acad Sci U S A, 95,
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The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
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Nat Struct Biol, 5,
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PDB codes:
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A.Pingoud,
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PDB codes:
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Cell, 83,
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Mol Microbiol, 13,
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Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy.
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EMBO J, 13,
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PDB codes:
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S.A.Smith,
S.B.Rajur,
and
L.W.McLaughlin
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Specific purine N7-nitrogens are critical for high affinity binding by the trp repressor.
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Nat Struct Biol, 1,
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S.K.Burley
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Plus ça change, plus c'est la même chose.
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Nat Struct Biol, 1,
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S.Kumar,
R.J.Roberts,
and
X.Cheng
(1994).
HhaI methyltransferase flips its target base out of the DNA helix.
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| |
Cell, 76,
357-369.
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PDB code:
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T.Liu,
E.F.DeRose,
and
G.P.Mullen
(1994).
Determination of the structure of the DNA binding domain of gamma delta resolvase in solution.
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| |
Protein Sci, 3,
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PDB codes:
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V.Ramesh,
R.O.Frederick,
S.E.Syed,
C.F.Gibson,
J.C.Yang,
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The interactions of Escherichia coli trp repressor with tryptophan and with an operator oligonucleotide. NMR studies using selectively 15N-labelled protein.
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Eur J Biochem, 225,
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W.J.Gehring,
Y.Q.Qian,
M.Billeter,
K.Furukubo-Tokunaga,
A.F.Schier,
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M.Affolter,
G.Otting,
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Homeodomain-DNA recognition.
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Cell, 78,
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W.K.Maas
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The arginine repressor of Escherichia coli.
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Microbiol Rev, 58,
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I.G.Old,
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The Met repressor-operator complex: DNA recognition by beta-strands.
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Ann N Y Acad Sci, 726,
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A.J.Bendall,
R.A.Sturm,
P.A.Danoy,
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Broad binding-site specificity and affinity properties of octamer 1 and brain octamer-binding proteins.
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Eur J Biochem, 217,
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B.T.Koh,
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A Simple genetically structured model of trp repressor-operator interactions.
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The SRY high-mobility-group box recognizes DNA by partial intercalation in the minor groove: a topological mechanism of sequence specificity.
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D.E.Lewis,
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Analysis of trp repressor-DNA interactions using gel electrophoresis.
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