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PDBsum entry 3orc

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protein dna_rna links
Gene regulation/DNA PDB id
3orc
Jmol
Contents
Protein chain
65 a.a. *
DNA/RNA
Waters ×3
* Residue conservation analysis
PDB id:
3orc
Name: Gene regulation/DNA
Title: Crystal structure of an engineered cro monomer bound nonspecifically to DNA
Structure: DNA (5'-d( Tp Ap Tp Cp Gp Ap Tp A)-3'). Chain: r, s. Engineered: yes. Other_details: 50% occupancy in the outermost positions. Protein (cro repressor). Chain: a. Engineered: yes. Mutation: yes. Other_details: wildtype cro does not form stable monomers.
Source: Synthetic: yes. Enterobacteria phage lambda. Organism_taxid: 10710. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.00Å     R-factor:   0.224    
Authors: R.A.Albright,M.C.Mossing,B.W.Matthews
Key ref:
R.A.Albright et al. (1998). Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein. Protein Sci, 7, 1485-1494. PubMed id: 9684880 DOI: 10.1002/pro.5560070701
Date:
23-Apr-98     Release date:   02-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03040  (RCRO_LAMBD) -  Regulatory protein cro
Seq:
Struc:
66 a.a.
65 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1002/pro.5560070701 Protein Sci 7:1485-1494 (1998)
PubMed id: 9684880  
 
 
Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein.
R.A.Albright, M.C.Mossing, B.W.Matthews.
 
  ABSTRACT  
 
The structure has been determined at 3.0 A resolution of a complex of engineered monomeric Cro repressor with a seven-base pair DNA fragment. Although the sequence of the DNA corresponds to the consensus half-operator that is recognized by each subunit of the wild-type Cro dimer, the complex that is formed in the crystals by the isolated monomer appears to correspond to a sequence-independent mode of association. The overall orientation of the protein relative to the DNA is markedly different from that observed for Cro dimer bound to a consensus operator. The recognition helix is rotated 48 degrees further out of the major groove, while the turn region of the helix-turn-helix remains in contact with the DNA backbone. All of the direct base-specific interactions seen in the wild-type Cro-operator complex are lost. Virtually all of the ionic interactions with the DNA backbone, however, are maintained, as is the subset of contacts between the DNA backbone and a channel on the protein surface. Overall, 25% less surface area is buried at the protein DNA interface than for half of the wild-type Cro-operator complex, and the contacts are more ionic in character due to a reduction of hydrogen bonding and van der Waals interactions. Based on this crystal structure, model building was used to develop a possible model for the sequence-nonspecific interaction of the wild-type Cro dimer with DNA. In the sequence-specific complex, the DNA is bent, the protein dimer undergoes a large hinge-bending motion relative to the uncomplexed form, and the complex is twofold symmetric. In contrast, in the proposed nonspecific complex the DNA is straight, the protein retains a conformation similar to the apo form, and the complex lacks twofold symmetry. The model is consistent with thermodynamic, chemical, and mutagenic studies, and suggests that hinge bending of the Cro dimer may be critical in permitting the transition from the binding of protein at generic sites on the DNA to binding at high affinity operator sites.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo figure showing the electron density in the region where the sugar-phosphatebackbone oftheDNA (yellow)passes through thechanelonthe surface of the Cro monomer(white).Thepart of theproteinshownincludesPhe58,whichpenetratesinto thehydrophobic core, andtheC-terminalresidues(toAsn61).whichoccupytheminorgroove of he NA. Coefficients are 2F0 - F, andphases are from the refmedmodel The map is contouredat lm.
Figure 8.
Fig. 8. Comparison of thebinding f Crotooperator DNA withtheten- tativemodel for the bindingtononcognate DNA. A: Themodelfornon- specificbindingvewedperpendiculartothe DNA (c.f. Fig. 7A). The right-handmonomer is alignedonthe DNA asinthecomplexof he engineeredCromonomer.Theremainder ofthe dimerwasbuiltassuming theconformation f wild-typeCr(Andersonet al., 1981;Ohlendorfet al., 1998).Terecognitionhelices of bothmonomers,shown in red,arecose to the DNA, butthe contactsaremade y opposite ends fthe helices, and are not equivalent. B: Binding of wild-typeCrotooperator DNA (from Albright & atthews,
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1998, 7, 1485-1494) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20375284 I.E.Sánchez, D.U.Ferreiro, M.Dellarole, and G.de Prat-Gay (2010).
Experimental snapshots of a protein-DNA binding landscape.
  Proc Natl Acad Sci U S A, 107, 7751-7756.  
17284455 H.Tjong, and H.X.Zhou (2007).
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.
  Nucleic Acids Res, 35, 1465-1477.  
17437717 S.A.Townson, J.C.Samuelson, Y.Bao, S.Y.Xu, and A.K.Aggarwal (2007).
BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning.
  Structure, 15, 449-459.
PDB code: 2p0j
15894630 M.Fuxreiter, M.Mezei, I.Simon, and R.Osman (2005).
Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.
  Biophys J, 89, 903-911.  
12784213 J.Aishima, and C.Wolberger (2003).
Insights into nonspecific binding of homeodomains from a structure of MATalpha2 bound to DNA.
  Proteins, 51, 544-551.  
12719261 J.Sun, H.Viadiu, A.K.Aggarwal, and H.Weinstein (2003).
Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex.
  Biophys J, 84, 3317-3325.  
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.  
11159430 A.H.Elcock, and J.A.McCammon (2001).
Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient.
  Biophys J, 80, 613-625.  
11599025 O.Littlefield, and H.C.Nelson (2001).
Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex.
  Proteins, 45, 219-228.
PDB codes: 1fyk 1fyl 1fym
11514661 W.A.Breyer, and B.W.Matthews (2001).
A structural basis for processivity.
  Protein Sci, 10, 1699-1711.  
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