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PDBsum entry 1wrs
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Complex (operon repressor/peptide) PDB id
1wrs

 

 

 

 

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Contents
Protein chains
104 a.a. *
Ligands
TRP ×2
* Residue conservation analysis
PDB id:
1wrs
Name: Complex (operon repressor/peptide)
Title: Nmr study of holo trp repressor
Structure: Holo trp repressor. Chain: r, s
Source: Escherichia coli. Organism_taxid: 562. Strain: cy15070 and cy17071
NMR struc: 15 models
Authors: D.Zhao,Z.Zheng
Key ref: D.Zhao et al. (1993). Refined solution structures of the Escherichia coli trp holo- and aporepressor. J Mol Biol, 229, 735-746. PubMed id: 8433368
Date:
12-May-95     Release date:   20-Jun-96    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A881  (TRPR_ECOLI) -  Trp operon repressor from Escherichia coli (strain K12)
Seq:
Struc: 		108 a.a.
104 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
J Mol Biol 229:735-746 (1993)
PubMed id: 8433368  
 
 
Refined solution structures of the Escherichia coli trp holo- and aporepressor.
D.Zhao, C.H.Arrowsmith, X.Jia, O.Jardetzky.
 
  ABSTRACT  
 
The solution structures of the trp-repressor from Escherichia coli in both the liganded (holo-) and unliganded (apo-) form, have been refined by restrained molecular dynamics with simulated annealing using the program XPLOR and additional experimental constraints. The ensemble of refined holorepressor structures have a root-mean-square deviation (r.m.s.d.) of 0.8 A relative to the average structure for the backbone of the dimer core (helices A, B, C, A', B', C') and 2.5 A for the helix-turn-helix DNA-binding domain (helices D and E). The corresponding values for the aporepressor are 0.9 A for the backbone of the ABC-dimer core and 3.2 A for the DE helix-turn-helix. The r.m.s.d. of the average structures from the corresponding crystal structures are 2.3 A for the holorepressor ABC core and 4.2 A for its DE region; 2.3 A for the aporepressor core and 5.5 A for its DE region. The relative disorder of the DNA-binding domain is reflected in a number of experimental parameters including substantially more rapid backbone proton exchange rates, exchange-limited relaxation times and crystallographic B-factors. The stabilizing effect of the L-Trp ligand is evident in these measurements, as it is in the higher precision of the holorepressor structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20080782 D.Beckett (2009).
Regulating transcription regulators via allostery and flexibility.
  Proc Natl Acad Sci U S A, 106, 22035-22036.  
17407165 K.S.Sandhu, and D.Dash (2007).
Dynamic alpha-helices: conformations that do not conform.
  Proteins, 68, 109-122.  
16738132 V.Payal, and P.Gollnick (2006).
Substitutions of Thr30 provide mechanistic insight into tryptophan-mediated activation of TRAP binding to RNA.
  Nucleic Acids Res, 34, 2933-2942.  
15274929 C.L.Lawson, B.Benoff, T.Berger, H.M.Berman, and J.Carey (2004).
E. coli trp repressor forms a domain-swapped array in aqueous alcohol.
  Structure, 12, 1099-1108.
PDB code: 1mi7
15382234 K.Gunasekaran, B.Ma, and R.Nussinov (2004).
Is allostery an intrinsic property of all dynamic proteins?
  Proteins, 57, 433-443.  
11180561 A.P.Demchenko (2001).
Recognition between flexible protein molecules: induced and assisted folding.
  J Mol Recognit, 14, 42-61.  
10465773 A.Wallqvist, T.A.Lavoie, J.A.Chanatry, D.G.Covell, and J.Carey (1999).
Cooperative folding units of escherichia coli tryptophan repressor.
  Biophys J, 77, 1619-1626.  
10518785 M.Jeeves, P.D.Evans, R.A.Parslow, M.Jaseja, and E.I.Hyde (1999).
Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences.
  Eur J Biochem, 265, 919-928.  
9843406 L.M.Gloss, and C.R.Matthews (1998).
Mechanism of folding of the dimeric core domain of Escherichia coli trp repressor: a nearly diffusion-limited reaction leads to the formation of an on-pathway dimeric intermediate.
  Biochemistry, 37, 15990-15999.  
9843407 L.M.Gloss, and C.R.Matthews (1998).
The barriers in the bimolecular and unimolecular folding reactions of the dimeric core domain of Escherichia coli Trp repressor are dominated by enthalpic contributions.
  Biochemistry, 37, 16000-16010.  
  9655343 N.Potier, L.J.Donald, I.Chernushevich, A.Ayed, W.Ens, C.H.Arrowsmith, K.G.Standing, and H.W.Duckworth (1998).
Study of a noncovalent trp repressor: DNA operator complex by electrospray ionization time-of-flight mass spectrometry.
  Protein Sci, 7, 1388-1395.  
9570398 S.G.Mackintosh, P.F.McDermott, and B.K.Hurlburt (1998).
Mutational analysis of the NH2-terminal arms of the trp repressor indicates a multifunctional domain.
  Mol Microbiol, 27, 1119-1127.  
9354760 D.Szwajkajzer, and J.Carey (1997).
Molecular and biological constraints on ligand-binding affinity and specificity.
  Biopolymers, 44, 181-198.  
9287161 H.Berglund, M.Wolf-Watz, T.Lundbäck, S.van den Berg, and T.Härd (1997).
Structure and dynamics of the glucocorticoid receptor DNA-binding domain: comparison of wild type and a mutant with altered specificity.
  Biochemistry, 36, 11188-11197.  
9154911 H.N.Moseley, W.Lee, C.H.Arrowsmith, and N.R.Krishna (1997).
Quantitative determination of conformational, dynamic, and kinetic parameters of a ligand-protein/DNA complex from a complete relaxation and conformational exchange matrix analysis of intermolecular transferred NOESY.
  Biochemistry, 36, 5293-5299.  
9236009 J.Zurdo, J.M.Sanz, C.González, M.Rico, and J.P.Ballesta (1997).
The exchangeable yeast ribosomal acidic protein YP2beta shows characteristics of a partly folded state under physiological conditions.
  Biochemistry, 36, 9625-9635.  
9153401 L.M.Gloss, and C.R.Matthews (1997).
Urea and thermal equilibrium denaturation studies on the dimerization domain of Escherichia coli Trp repressor.
  Biochemistry, 36, 5612-5623.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
  8897612 C.J.Morton, and J.E.Ladbury (1996).
Water-mediated protein-DNA interactions: the relationship of thermodynamics to structural detail.
  Protein Sci, 5, 2115-2118.  
8946848 C.L.Lawson (1996).
An atomic view of the L-tryptophan binding site of trp repressor.
  Nat Struct Biol, 3, 986-987.
PDB code: 1jhg
8552675 G.M.Verkhivker, and P.A.Rejto (1996).
A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding.
  Proc Natl Acad Sci U S A, 93, 60-64.  
  8845754 M.D.Finucane, and O.Jardetzky (1996).
The pH dependence of hydrogen-deuterium exchange in trp repressor: the exchange rate of amide protons in proteins reflects tertiary interactions, not only secondary structure.
  Protein Sci, 5, 653-662.  
  8762153 M.R.Gryk, O.Jardetzky, L.S.Klig, and C.Yanofsky (1996).
Flexibility of DNA binding domain of trp repressor required for recognition of different operator sequences.
  Protein Sci, 5, 1195-1197.  
9022683 P.D.Evans, M.Jaseja, M.Jeeves, and E.I.Hyde (1996).
NMR studies of the Escherichia coli Trp repressor.trpRs operator complex.
  Eur J Biochem, 242, 567-575.  
17029807 T.Härd, and T.Lundbäck (1996).
Thermodynamics of sequence-specific protein-DNA interactions.
  Biophys Chem, 62, 121-139.  
8654432 V.Ramesh, S.E.Syed, R.O.Frederick, M.J.Sutcliffe, M.Barnes, and G.C.Roberts (1996).
NMR studies of the mode of binding of corepressors and inducers to Escherichia coli trp repressor.
  Eur J Biochem, 235, 804-813.  
8747435 Z.Blicharska, and Z.Wasylewski (1995).
Fluorescence quenching studies of Trp repressor using single-tryptophan mutants.
  J Protein Chem, 14, 739-746.  
8208606 D.N.Arvidson, C.G.Arvidson, C.L.Lawson, J.Miner, C.Adams, and P.Youderian (1994).
The tryptophan repressor sequence is highly conserved among the Enterobacteriaceae.
  Nucleic Acids Res, 22, 1821-1829.  
7854115 J.Pfau, D.N.Arvidson, and P.Youderian (1994).
Mutants of Escherichia coli Trp repressor with changes of conserved, helix-turn-helix residue threonine 81 have altered DNA-binding specificities.
  Mol Microbiol, 13, 1001-1012.  
8183906 S.Bagby, T.S.Harvey, S.G.Eagle, S.Inouye, and M.Ikura (1994).
Structural similarity of a developmentally regulated bacterial spore coat protein to beta gamma-crystallins of the vertebrate eye lens.
  Proc Natl Acad Sci U S A, 91, 4308-4312.  
7957174 V.Ramesh, R.O.Frederick, S.E.Syed, C.F.Gibson, J.C.Yang, and G.C.Roberts (1994).
The interactions of Escherichia coli trp repressor with tryptophan and with an operator oligonucleotide. NMR studies using selectively 15N-labelled protein.
  Eur J Biochem, 225, 601-608.  
7892173 Y.Komeiji, M.Uebayasi, and I.Yamato (1994).
Molecular dynamics simulations of trp apo- and holorepressors: domain structure and ligand-protein interaction.
  Proteins, 20, 248-258.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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