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DNA binding regulatory protein PDB id
1lrp
Jmol
Contents
Protein chains
89 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1lrp
Name: DNA binding regulatory protein
Title: Comparison of the structures of cro and lambda repressor pro bacteriophage lambda
Structure: Lambda repressor. Chain: a, b, c. Engineered: yes
Source: Enterobacteria phage lambda. Organism_taxid: 10710
Biol. unit: Dimer (from PQS)
Resolution:
3.20Å     R-factor:   not given    
Authors: C.Pabo,M.Lewis
Key ref:
D.H.Ohlendorf et al. (1983). Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda. J Mol Biol, 169, 757-769. PubMed id: 6226802 DOI: 10.1016/S0022-2836(83)80169-7
Date:
04-Dec-87     Release date:   09-Jan-89    
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03034  (RPC1_LAMBD) -  Repressor protein CI
Seq:
Struc: 		237 a.a.
89 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA binding     2 terms  

 

 
    Key reference    
 
 
DOI no: 10.1016/S0022-2836(83)80169-7 J Mol Biol 169:757-769 (1983)
PubMed id: 6226802  
 
 
Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda.
D.H.Ohlendorf, W.F.Anderson, M.Lewis, C.O.Pabo, B.W.Matthews.
 
  ABSTRACT  
 
The three-dimensional structures of cro repressor protein and of the amino-terminal domain of lambda repressor protein, both from bacteriophage lambda, are compared. The second and third alpha-helices, alpha 2 and alpha 3, are shown to have essentially identical conformations in the two proteins, confirming the significance of the amino acid sequence homology previously noted between these and other DNA binding proteins in the region corresponding to these helices. The correspondence between the two-helical units in cro and lambda repressor protein is better than the striking agreement noted previously between two-helical units in cro and catabolite gene-activator protein. Parts of the first alpha-helices of repressor and cro show a structural correspondence that suggests a revised sequence homology between the two proteins in their extreme amino-terminal regions. In particular, there is a short loop between the alpha 1 and alpha 2 helices of lambda repressor that is missing from cro. This structural difference may account for the observed differences found with different cros and repressors in the pattern of phosphates whose ethylation prevents the binding of these proteins to their specific recognition sites. Although the two proteins have strikingly similar alpha 2-alpha 3 helical units that are presumed to bind to DNA in an essentially similar manner, stereochemical restrictions prevent the alpha 2-alpha 3 units of the respective proteins aligning on the DNA in exactly the same way.
 
  Selected figure(s)  
 
Figure 7.
FIo. 7. Hypothetical dimem of cro and A repressor constructed as described in he text. (a) Hypothetical mpressor dimer. onomers of A repressor placed so that theira2-~ 3 helices coincide with the a2-a3 helices in a cro dimer. One monomer of A repressor is drawn filled, theothr open. Thin lines represet te cro dimer. (b) Hyothetical cro dimer. Monomers of cro paced with their a2-a3 helices coinident with the ~2-a3 helices in a A repressordimer. One monomer of cro drawn open, the other filled. Thin lines represent the A repressor dimer.
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (1983, 169, 757-769) copyright 1983.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
11297428 H.Matsuno, K.Niikura, and Y.Okahata (2001).
Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A.T base pairs of oligonucleotides immobilized on a 27 mhz quartz crystal microbalance.
  Biochemistry, 40, 3615-3622.  
10195898 M.H.Cordes, N.P.Walsh, C.J.McKnight, and R.T.Sauer (1999).
Evolution of a protein fold in vitro.
  Science, 284, 325-328.
PDB code: 1qtg
9520383 R.A.Albright, and B.W.Matthews (1998).
How Cro and lambda-repressor distinguish between operators: the structural basis underlying a genetic switch.
  Proc Natl Acad Sci U S A, 95, 3431-3436.  
9437426 T.L.Smith (1998).
Cro, CAP and lambda repressor led the way.
  Nat Struct Biol, 5, 29.  
7744019 P.Shore, and A.D.Sharrocks (1995).
The MADS-box family of transcription factors.
  Eur J Biochem, 229, 1.  
  8417320 A.D.Sharrocks, H.Gille, and P.E.Shaw (1993).
Identification of amino acids essential for DNA binding and dimerization in p67SRF: implications for a novel DNA-binding motif.
  Mol Cell Biol, 13, 123-132.  
8471062 V.Scarlato, B.Aricó, M.Domenighini, and R.Rappuoli (1993).
Environmental regulation of virulence factors in Bordetella species.
  Bioessays, 15, 99.  
  2185227 A.Sunnarborg, D.Klumpp, T.Chung, and D.C.LaPorte (1990).
Regulation of the glyoxylate bypass operon: cloning and characterization of iclR.
  J Bacteriol, 172, 2642-2649.  
2191698 P.E.Nielsen (1990).
Chemical and photochemical probing of DNA complexes.
  J Mol Recognit, 3, 1.  
2146682 R.G.Brennan, S.L.Roderick, Y.Takeda, and B.W.Matthews (1990).
Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex.
  Proc Natl Acad Sci U S A, 87, 8165-8169.
PDB code: 4cro
2269288 R.M.Lamerichs, R.Boelens, G.A.Van der Marel, J.H.Van Boom, and R.Kaptein (1990).
Assignment of the 1H-NMR spectrum of a lac repressor headpiece-operator complex in H2O and identification of NOEs. Consequences for protein-DNA interaction.
  Eur J Biochem, 194, 629-637.  
2204954 T.A.Steitz (1990).
Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding.
  Q Rev Biophys, 23, 205-280.  
2780540 A.A.Pakula, and R.T.Sauer (1989).
Amino acid substitutions that increase the thermal stability of the lambda Cro protein.
  Proteins, 5, 202-210.  
2552443 A.M.Brown, and D.M.Crothers (1989).
Modulation of the stability of a gene-regulatory protein dimer by DNA and cAMP.
  Proc Natl Acad Sci U S A, 86, 7387-7391.  
  2521838 N.Benson, and P.Youderian (1989).
Phage lambda Cro protein and cI repressor use two different patterns of specific protein-DNA interactions to achieve sequence specificity in vivo.
  Genetics, 121, 5.  
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.  
3185709 C.Wolberger, Y.C.Dong, M.Ptashne, and S.C.Harrison (1988).
Structure of a phage 434 Cro/DNA complex.
  Nature, 335, 789-795.  
  2907480 G.Otting, Y.Q.Qian, M.Müller, M.Affolter, W.Gehring, and K.Wüthrich (1988).
Secondary structure determination for the Antennapedia homeodomain by nuclear magnetic resonance and evidence for a helix-turn-helix motif.
  EMBO J, 7, 4305-4309.  
2946418 A.Hochschild, J.Douhan, and M.Ptashne (1986).
How lambda repressor and lambda Cro distinguish between OR1 and OR3.
  Cell, 47, 807-816.  
3086838 A.Wissmann, I.Meier, L.V.Wray, M.Geissendörfer, and W.Hillen (1986).
Tn10 tet operator mutations affecting Tet repressor recognition.
  Nucleic Acids Res, 14, 4253-4266.  
  3009392 B.B.Finlay, L.S.Frost, and W.Paranchych (1986).
Nucleotide sequences of the R1-19 plasmid transfer genes traM, finP, traJ, and traY and the traYZ promoter.
  J Bacteriol, 166, 368-374.  
3011275 L.Jen-Jacobson, D.Lesser, and M.Kurpiewski (1986).
The enfolding arms of EcoRI endonuclease: role in DNA binding and cleavage.
  Cell, 45, 619-629.  
  3881391 G.Klock, B.Unger, C.Gatz, W.Hillen, J.Altenbuchner, K.Schmid, and R.Schmitt (1985).
Heterologous repressor-operator recognition among four classes of tetracycline resistance determinants.
  J Bacteriol, 161, 326-332.  
3161621 H.C.Nelson, and R.T.Sauer (1985).
Lambda repressor mutations that increase the affinity and specificity of operator binding.
  Cell, 42, 549-558.  
3996412 M.F.Macchiato, V.Cuomo, and A.Tramontano (1985).
Determination of the autocorrelation orders of proteins.
  Eur J Biochem, 149, 375-379.  
  2988943 P.Argos (1985).
Evidence for a repeating domain in type I restriction enzymes.
  EMBO J, 4, 1351-1355.  
2994067 P.J.Isackson, and K.P.Bertrand (1985).
Dominant negative mutations in the Tn10 tet repressor: evidence for use of the conserved helix-turn-helix motif in DNA binding.
  Proc Natl Acad Sci U S A, 82, 6226-6230.  
6377305 I.T.Weber, and T.A.Steitz (1984).
Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity.
  Proc Natl Acad Sci U S A, 81, 3973-3977.
PDB code: 2gap
6390343 I.T.Weber, and T.A.Steitz (1984).
A model for the non-specific binding of catabolite gene activator protein to DNA.
  Nucleic Acids Res, 12, 8475-8487.  
6366744 L.Altschmied, and W.Hillen (1984).
TET repressor.tet operator complex formation induces conformational changes in the tet operator DNA.
  Nucleic Acids Res, 12, 2171-2180.  
6442995 L.H.Weaver, M.G.Grütter, S.J.Remington, T.M.Gray, N.W.Isaacs, and B.W.Matthews (1984).
Comparison of goose-type, chicken-type, and phage-type lysozymes illustrates the changes that occur in both amino acid sequence and three-dimensional structure during evolution.
  J Mol Evol, 21, 97.  
  6236998 M.P.Kirpichnikov, A.V.Kurochkin, B.K.Chernov, and K.G.Skryabin (1984).
Interactions between cro repressor and the model specific binding site.
  FEBS Lett, 175, 317-320.  
6390433 R.H.Ebright, P.Cossart, B.Gicquel-Sanzey, and J.Beckwith (1984).
Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity.
  Proc Natl Acad Sci U S A, 81, 7274-7278.  
6540625 R.P.Wharton, E.L.Brown, and M.Ptashne (1984).
Substituting an alpha-helix switches the sequence-specific DNA interactions of a repressor.
  Cell, 38, 361-369.  
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.