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protein dna_rna Protein-protein interface(s) links
Gene regulation/DNA PDB id
1rpe
Jmol
Contents
Protein chains
63 a.a. *
DNA/RNA
Waters ×36
* Residue conservation analysis
PDB id:
1rpe
Name: Gene regulation/DNA
Title: The phage 434 or2/r1-69 complex at 2.5 angstroms resolution
Structure: DNA (5'- d( Tp Ap Tp Ap Cp Ap Ap Tp Gp Tp Ap Tp Cp Tp Tp Gp T p Tp Tp G)-3'). Chain: b. Engineered: yes. DNA (5'- d( Ap Cp Ap Ap Ap Cp Ap Ap Gp Ap Tp Ap Cp Ap Tp Tp G p Tp Ap T)-3'). Chain: a.
Source: Synthetic: yes. Phage 434. Organism_taxid: 10712
Biol. unit: Homo-Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.209    
Authors: L.J.W.Shimon,S.C.Harrison
Key ref: L.J.Shimon and S.C.Harrison (1993). The phage 434 OR2/R1-69 complex at 2.5 A resolution. J Mol Biol, 232, 826-838. PubMed id: 8355273 DOI: 10.1006/jmbi.1993.1434
Date:
24-Mar-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P16117  (RPC1_BP434) -  Repressor protein CI (Fragment)
Seq:
Struc: 		95 a.a.
63 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1006/jmbi.1993.1434 J Mol Biol 232:826-838 (1993)
PubMed id: 8355273  
 
 
The phage 434 OR2/R1-69 complex at 2.5 A resolution.
L.J.Shimon, S.C.Harrison.
 
  ABSTRACT  
 
The crystal structure of the DNA-binding domain of bacteriophage 434 repressor (R1-69) in complex with a 20 base-pair DNA fragment has been determined to 2.5 A resolution. The DNA fragment contains the sequence of the OR2 operator site, which differs from the previously studied OR1 site at three of the variable six central base-pairs. Comparison of the two structures shows that the overall bent conformation of the DNA backbone as well as the pattern of DNA-protein interactions seen in the OR1/R1-69 complex are maintained in the OR2 complex. However, the conformations of the DNA base-pairs are different in the two structures. In particular, the central base-pairs of OR2/R1-69 structure are more co-planar than in OR1/R1-69, and there are no cross-strand "bifurcated" hydrogen bonds. These results show that binding of the protein causes operator DNA to adopt a particular, well-defined backbone conformation, and they reinforce the notion that the energetic cost of achieving this conformation, most likely different for different sequences, can determine, at least in part, the relative affinity of the repressor for different operator sites.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19019826 S.Russo, J.E.Schweitzer, T.Polen, M.Bott, and E.Pohl (2009).
Crystal structure of the caseinolytic protease gene regulator, a transcriptional activator in actinomycetes.
  J Biol Chem, 284, 5208-5216.
PDB codes: 3f51 3f52
16475182 J.Seetharaman, D.Kumaran, J.B.Bonanno, S.K.Burley, and S.Swaminathan (2006).
Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis.
  Proteins, 63, 1087-1091.
PDB code: 1sgm
17038333 N.B.Becker, L.Wolff, and R.Everaers (2006).
Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.
  Nucleic Acids Res, 34, 5638-5649.  
16897298 S.J.Williamson, and J.H.Paul (2006).
Environmental factors that influence the transition from lysogenic to lytic existence in the phiHSIC/Listonella pelagia marine phage-host system.
  Microb Ecol, 52, 217-225.  
16338412 M.R.Sawaya, Z.Zhu, F.Mersha, S.H.Chan, R.Dabur, S.Y.Xu, and G.K.Balendiran (2005).
Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site.
  Structure, 13, 1837-1847.
PDB code: 2b5a
15753294 M.Radman-Livaja, T.Biswas, D.Mierke, and A.Landy (2005).
Architecture of recombination intermediates visualized by in-gel FRET of lambda integrase-Holliday junction-arm DNA complexes.
  Proc Natl Acad Sci U S A, 102, 3913-3920.  
14679217 D.R.Pawlowski, and G.B.Koudelka (2004).
The preferred substrate for RecA-mediated cleavage of bacteriophage 434 repressor is the DNA-bound dimer.
  J Bacteriol, 186, 1-7.  
15359276 S.Rumpel, A.Razeto, C.M.Pillar, V.Vijayan, A.Taylor, K.Giller, M.S.Gilmore, S.Becker, and M.Zweckstetter (2004).
Structure and DNA-binding properties of the cytolysin regulator CylR2 from Enterococcus faecalis.
  EMBO J, 23, 3632-3642.
PDB code: 1utx
12548627 B.Hartmann, M.R.Sullivan, and L.F.Harris (2003).
Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50-bp DNA reveal important differences between the OR1 and OR2 sites.
  Biopolymers, 68, 250-264.  
12569094 S.A.Mauro, D.Pawlowski, and G.B.Koudelka (2003).
The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor.
  J Biol Chem, 278, 12955-12960.  
11972345 K.Steinmetzer, J.Behlke, S.Brantl, and M.Lorenz (2002).
CopR binds and bends its target DNA: a footprinting and fluorescence resonance energy transfer study.
  Nucleic Acids Res, 30, 2052-2060.  
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
10766954 D.C.Kombo, M.A.Young, and D.L.Beveridge (2000).
One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein.
  Biopolymers, 53, 596-605.  
10561603 G.Caderas, S.Klauser, N.Liu, A.Bienz, and B.Gutte (1999).
Inhibition of HIV-1 enhancer-controlled transcription by artificial enhancer-binding peptides derived from bacteriophage 434 repressor.
  Eur J Biochem, 266, 599-607.  
9788911 J.Woda, B.Schneider, K.Patel, K.Mistry, and H.M.Berman (1998).
An analysis of the relationship between hydration and protein-DNA interactions.
  Biophys J, 75, 2170-2177.  
9727039 J.Xu, and G.B.Koudelka (1998).
DNA-based positive control mutants in the binding site sequence of 434 repressor.
  J Biol Chem, 273, 24165-24172.  
9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
  Nucleic Acids Res, 26, 1906-1926.  
9153301 J.Chen, S.Pongor, and A.Simoncsits (1997).
Recognition of DNA by single-chain derivatives of the phage 434 repressor: high affinity binding depends on both the contacted and non-contacted base pairs.
  Nucleic Acids Res, 25, 2047-2054.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
9218422 M.Oda, K.Furukawa, K.Ogata, A.Sarai, S.Ishii, Y.Nishimura, and H.Nakamura (1997).
Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.
  J Biol Chem, 272, 17966-17971.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
  8755874 D.B.Diep, L.S.Håvarstein, and I.F.Nes (1996).
Characterization of the locus responsible for the bacteriocin production in Lactobacillus plantarum C11.
  J Bacteriol, 178, 4472-4483.  
7836381 A.C.Bell, and G.B.Koudelka (1995).
How 434 repressor discriminates between OR1 and OR3. The influence of contacted and noncontacted base pairs.
  J Biol Chem, 270, 1205-1212.  
  7737131 I.Brukner, R.Sánchez, D.Suck, and S.Pongor (1995).
Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.
  EMBO J, 14, 1812-1818.  
  7735836 J.W.Schwabe, L.Chapman, and D.Rhodes (1995).
The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation.
  Structure, 3, 201-213.  
7647248 M.A.Young, G.Ravishanker, D.L.Beveridge, and H.M.Berman (1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
  Biophys J, 68, 2454-2468.  
8749848 M.Suzuki, and M.Gerstein (1995).
Binding geometry of alpha-helices that recognize DNA.
  Proteins, 23, 525-535.  
7610037 M.Suzuki, and N.Yagi (1995).
Stereochemical basis of DNA bending by transcription factors.
  Nucleic Acids Res, 23, 2083-2091.  
7664086 N.D.Arbuckle, and B.Luisi (1995).
A recipe for specificity.
  Nat Struct Biol, 2, 341-346.  
  8590003 T.E.Strzelecka, G.M.Clore, and A.M.Gronenborn (1995).
The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif.
  Structure, 3, 1087-1095.
PDB codes: 1neq 1ner
  8081737 D.W.Rodgers, and S.C.Harrison (1993).
The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.
  Structure, 1, 227-240.
PDB code: 1per
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 codes are shown on the right.