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PDBsum entry 2oz9
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protein ligands metals links
DNA binding protein PDB id
2oz9

 

 

 

 

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Contents
Protein chain
104 a.a. *
Ligands
SO4
TRP
Metals
_NA
Waters ×85
* Residue conservation analysis
PDB id:
2oz9
Name: DNA binding protein
Title: E. Coli trp holorepressor, orthorhombic crystal form
Structure: Trp operon repressor. Chain: r. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: trpr, rtry. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.65Å     R-factor:   0.180    
Authors: C.L.Lawson,P.B.Sigler
Key ref: C.L.Lawson et al. (1988). Flexibility of the DNA-binding domains of trp repressor. Proteins, 3, 18-31. PubMed id: 3375234
Date:
25-Feb-07     Release date:   06-Mar-07    
Supersedes: 2wrp
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
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

 

 
Proteins 3:18-31 (1988)
PubMed id: 3375234  
 
 
Flexibility of the DNA-binding domains of trp repressor.
C.L.Lawson, R.G.Zhang, R.W.Schevitz, Z.Otwinowski, A.Joachimiak, P.B.Sigler.
 
  ABSTRACT  
 
An orthorhombic crystal form of trp repressor (aporepressor plus L-tryptophan ligand) was solved by molecular replacement, refined to 1.65 A resolution, and compared to the structure of the repressor in trigonal crystals. Even though these two crystal forms of repressor were grown under identical conditions, the refined structures have distinctly different conformations of the DNA-binding domains. Unlike the repressor/aporepressor structural transition, the conformational shift is not caused by the binding or loss of the L-tryptophan ligand. We conclude that while L-tryptophan binding is essential for forming a specific complex with trp operator DNA, the corepressor ligand does not lock the repressor into a single conformation that is complementary to the operator. This flexibility may be required by the various binding modes proposed for trp repressor in its search for and adherence to its three different operator sites.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21049125 V.N.Uversky (2011).
Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes.
  Chem Soc Rev, 40, 1623-1634.  
20617196 H.Dong, S.Qin, and H.X.Zhou (2010).
Effects of macromolecular crowding on protein conformational changes.
  PLoS Comput Biol, 6, e1000833.  
16740123 A.Bhardwaj, K.Welfle, R.Misselwitz, S.Ayora, J.C.Alonso, and H.Welfle (2006).
Conformation and stability of the Streptococcus pyogenes pSM19035-encoded site-specific beta recombinase, and identification of a folding intermediate.
  Biol Chem, 387, 525-533.  
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
14530390 O.Millet, R.P.Hudson, and L.E.Kay (2003).
The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy.
  Proc Natl Acad Sci U S A, 100, 12700-12705.  
12144778 L.Claret, and C.Hughes (2002).
Interaction of the atypical prokaryotic transcription activator FlhD2C2 with early promoters of the flagellar gene hierarchy.
  J Mol Biol, 321, 185-199.  
10704223 T.A.Ramelot, L.N.Gentile, and L.K.Nicholson (2000).
Transient structure of the amyloid precursor protein cytoplasmic tail indicates preordering of structure for binding to cytosolic factors.
  Biochemistry, 39, 2714-2725.  
10969026 W.Wriggers, R.K.Agrawal, D.L.Drew, A.McCammon, and J.Frank (2000).
Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures.
  Biophys J, 79, 1670-1678.  
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.  
10450084 S.Hayward (1999).
Structural principles governing domain motions in proteins.
  Proteins, 36, 425-435.  
9722650 M.Gerstein, and W.Krebs (1998).
A database of macromolecular motions.
  Nucleic Acids Res, 26, 4280-4290.  
9235002 A.L.Lomize, and H.I.Mosberg (1997).
Thermodynamic model of secondary structure for alpha-helical peptides and proteins.
  Biopolymers, 42, 239-269.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
9242917 M.Levitt, M.Gerstein, E.Huang, S.Subbiah, and J.Tsai (1997).
Protein folding: the endgame.
  Annu Rev Biochem, 66, 549-579.  
8990498 N.Honda, Y.Komeiji, M.Uebayasi, and I.Yamato (1996).
Computational design of a substrate specificity mutant of a protein.
  Proteins, 26, 459-464.  
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.  
8805508 P.Thiyagarajan, S.J.Henderson, and A.Joachimiak (1996).
Solution structures of GroEL and its complex with rhodanese from small-angle neutron scattering.
  Structure, 4, 79-88.  
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.  
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.  
  7987223 J.Guenot, R.J.Fletterick, and P.A.Kollman (1994).
A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA.
  Protein Sci, 3, 1276-1285.  
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.  
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.  
8265562 M.Hilbert, G.Böhm, and R.Jaenicke (1993).
Structural relationships of homologous proteins as a fundamental principle in homology modeling.
  Proteins, 17, 138-151.  
8284212 M.Shapiro, D.N.Arvidson, J.Pfau, and P.Youderian (1993).
The challenge-phage assay reveals differences in the binding equilibria of mutant Escherichia coli Trp super-repressors in vivo.
  Nucleic Acids Res, 21, 5661-5666.  
8497488 S.H.Bryant, and C.E.Lawrence (1993).
An empirical energy function for threading protein sequence through the folding motif.
  Proteins, 16, 92.  
8346192 Y.Komeiji, M.Uebayasi, J.Someya, and I.Yamato (1993).
A molecular dynamics study of solvent behavior around a protein.
  Proteins, 16, 268-277.  
  1304395 A.E.Howard, and P.A.Kollman (1992).
Molecular dynamics studies of a DNA-binding protein: 1. A comparison of the trp repressor and trp aporepressor aqueous simulations.
  Protein Sci, 1, 1173-1184.  
1322324 B.A.Lynch, and D.E.Koshland (1992).
The fifth Datta Lecture. Structural similarities between the aspartate receptor of bacterial chemotaxis and the trp repressor of E. coli. Implications for transmembrane signaling.
  FEBS Lett, 307, 3-9.  
  1304396 J.Guenot, and P.A.Kollman (1992).
Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.
  Protein Sci, 1, 1185-1205.  
1740124 K.L.Borden, C.J.Bauer, T.A.Frenkiel, P.Beckmann, and A.N.Lane (1992).
Sequence-specific NMR assignments of the trp repressor from Escherichia coli using three-dimensional 15N/1H heteronuclear techniques.
  Eur J Biochem, 204, 137-146.  
  1531047 N.Benson, C.Adams, and P.Youderian (1992).
Mutant lambda repressors with increased operator affinities reveal new, specific protein-DNA contacts.
  Genetics, 130, 17-26.  
  1639072 T.E.Haran, A.Joachimiak, and P.B.Sigler (1992).
The DNA target of the trp repressor.
  EMBO J, 11, 3021-3030.  
  2060777 D.N.Arvidson, M.Shapiro, and P.Youderian (1991).
Mutant tryptophan aporepressors with altered specificities of corepressor recognition.
  Genetics, 128, 29-35.  
1935952 E.I.Hyde, V.Ramesh, R.Frederick, and G.C.Roberts (1991).
NMR studies of the activation of the Escherichia coli trp repressor.
  Eur J Biochem, 201, 569-579.  
1841704 J.Czaplicki, C.Arrowsmith, and O.Jardetzky (1991).
Segmental differences in the stability of the trp-repressor peptide backbone.
  J Biomol NMR, 1, 349-361.  
1761046 K.L.Borden, P.Beckmann, and A.N.Lane (1991).
Determination of the orientations of tryptophan analogues bound to the trp repressor and the relationship to activation.
  Eur J Biochem, 202, 459-470.  
1971945 M.Affolter, A.Percival-Smith, M.Müller, W.Leupin, and W.J.Gehring (1990).
DNA binding properties of the purified Antennapedia homeodomain.
  Proc Natl Acad Sci U S A, 87, 4093-4097.  
2204954 T.A.Steitz (1990).
Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding.
  Q Rev Biophys, 23, 205-280.  
2499455 A.N.Lane (1989).
The influence of tryptophan on mobility of residues in the trp repressor of Escherichia coli.
  Eur J Biochem, 182, 95.  
2673778 E.I.Hyde, V.Ramesh, G.C.Roberts, C.H.Arrowsmith, L.Treat-Clemons, B.Klaic, and O.Jardetzky (1989).
NMR studies of the Escherichia coli trp aporepressor. Sequence-specific assignment of the aromatic proton resonances.
  Eur J Biochem, 183, 545-553.  
2675171 M.F.Perutz (1989).
Mechanisms of cooperativity and allosteric regulation in proteins.
  Q Rev Biophys, 22, 139-237.  
2572329 Y.Q.Qian, M.Billeter, G.Otting, M.Müller, W.J.Gehring, and K.Wüthrich (1989).
The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressors.
  Cell, 59, 573-580.  
2855370 J.S.Richardson, and D.C.Richardson (1988).
Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal.
  Proteins, 4, 229-239.  
3070558 T.J.Graddis, L.S.Klig, C.Yanofsky, and D.L.Oxender (1988).
Formation of heterodimers between wild type and mutant trp aporepressor polypeptides of Escherichia coli.
  Proteins, 4, 173-181.  
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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