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PDBsum entry 5cro

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protein ligands Protein-protein interface(s) links
Gene regulating protein PDB id
5cro
Jmol
Contents
Protein chains
60 a.a. *
Ligands
PO4 ×2
Waters ×33
* Residue conservation analysis
PDB id:
5cro
Name: Gene regulating protein
Title: Refined structure of cro repressor protein from bacteriophage lambda
Structure: Cro repressor protein. Chain: o, a, b, c. Other_details: water molecules and two phosphate radicals
Source: Enterobacteria phage lambda. Organism_taxid: 10710
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.193    
Authors: D.H.Ohlendorf,D.E.Tronrud,B.W.Matthews
Key ref:
D.H.Ohlendorf et al. (1998). Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity. J Mol Biol, 280, 129-136. PubMed id: 9653036 DOI: 10.1006/jmbi.1998.1849
Date:
17-Apr-98     Release date:   17-Jun-98    
Supersedes: 1cro
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03040  (RCRO_LAMBD) -  Regulatory protein cro
Seq:
Struc:
66 a.a.
60 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1006/jmbi.1998.1849 J Mol Biol 280:129-136 (1998)
PubMed id: 9653036  
 
 
Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity.
D.H.Ohlendorf, D.E.Tronrud, B.W.Matthews.
 
  ABSTRACT  
 
The structure of the Cro repressor protein from phage lambda has been refined to a crystallographic R-value of 19.3% at 2.3 A resolution. The re fined model supports the structure as originally described in 1981 and provides a basis for comparison with the Cro-operator complex described in the accompanying paper. Changes in structure seen in different crystal forms and modifications of Cro suggest that the individual subunits are somewhat plastic in nature. In addition, the dimer of Cro suggests a high degree of flexibility, which may be important in forming the Cro-DNA complex. The structure of the Cro subunit as determined by NMR agrees reasonably well with that in the crystals (root-mean-square discrepancy of about 2 A for all atoms). There are, however, only a limited number of intersubunit distance constraints and, presumably for this reason, the different NMR models for the dimer vary substantially among themselves (discrepancies of 1.3 to 5.5 A). Because of this variation it is not possible to say whether the range of discrepancies between the X-ray and NMR Cro dimers (2.9 to 7.5 A) represent a significant difference between the X-ray and solution structures. It has previously been proposed that substitutions of Tyr26 in Cro increase thermal stability by the "reverse hydrophobic effect", i.e. by exposing 40% more hydrophobic surface to solvent in the folded form than in the unfolded state. The refined structure, however, suggests that Tyr26 is equally solvent exposed in the folded and unfolded states. The most stabilizing substitution is Tyr26-->Asp and in this case it appears that interaction with an alpha-helix dipole is at least partly responsible for the enhanced stability.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Ramachandran diagram, calculated using the program of [Laskowski et al 1993], showing the backbone conformational angles for the four Cro monomers. Glycine residues are shown as triangles, non-glycine residues as squares. Ser60 is toward the carboxy terminus of the molecule at the point where the electron density becomes weak, indicative of disorder.
Figure 3.
Figure 3. Representative sections of the electron density map following refinement. Coefficients are 2F[o]−F[c], where F[o] are the observed amplitudes and F[c] are those calculated from the refined model. Phases also are from the refined model. (a) The region near cisPro59. The Figure includes the conserved water molecule, labeled Sol. (b) The region where Phe58 of monomer A (labeled A58) penetrates into the hydrophobic core of monomer C and is surrounded by residues, including Leu7, Leu23, Val25, Ile30, Arg38 and Ile40.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 280, 129-136) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19356231 J.Estrada, P.Bernadó, M.Blackledge, and J.Sancho (2009).
ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble.
  BMC Bioinformatics, 10, 104.  
18227506 C.G.Roessler, B.M.Hall, W.J.Anderson, W.M.Ingram, S.A.Roberts, W.R.Montfort, and M.H.Cordes (2008).
Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds.
  Proc Natl Acad Sci U S A, 105, 2343-2348.
PDB codes: 2pij 3bd1
18369196 M.S.Dubrava, W.M.Ingram, S.A.Roberts, A.Weichsel, W.R.Montfort, and M.H.Cordes (2008).
N15 Cro and lambda Cro: orthologous DNA-binding domains with completely different but equally effective homodimer interfaces.
  Protein Sci, 17, 803-812.
PDB code: 2hin
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.  
15062080 T.Newlove, J.H.Konieczka, and M.H.Cordes (2004).
Secondary structure switching in Cro protein evolution.
  Structure, 12, 569-581.
PDB code: 1rzs
12598646 K.R.LeFevre, and M.H.Cordes (2003).
Retroevolution of lambda Cro toward a stable monomer.
  Proc Natl Acad Sci U S A, 100, 2345-2350.  
10707026 K.Steinmetzer, A.Hillisch, J.Behlke, and S.Brantl (2000).
Transcriptional repressor CopR: structure model-based localization of the deoxyribonucleic acid binding motif.
  Proteins, 38, 393-406.  
10985796 P.J.Darling, J.M.Holt, and G.K.Ackers (2000).
Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding I: analysis of cro dimerization from nanomolar to micromolar concentrations.
  Biochemistry, 39, 11500-11507.  
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