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PDBsum entry 1zug

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protein links
Transcription regulation PDB id
1zug
Jmol PyMol
Contents
Protein chain
71 a.a. *
* Residue conservation analysis
PDB id:
1zug
Name: Transcription regulation
Title: Structure of phage 434 cro protein, nmr, 20 structures
Structure: Phage 434 cro protein. Chain: a. Engineered: yes
Source: Phage 434. Organism_taxid: 10712. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the plasmid was a gift from the laboratory of professor steve harrison (harvard university)
NMR struc: 20 models
Authors: S.Padmanabhan,M.A.Jimenez,C.Gonzalez,J.M.Sanz,G.Gimenez- Gallego,M.Rico
Key ref:
S.Padmanabhan et al. (1997). Three-dimensional solution structure and stability of phage 434 Cro protein. Biochemistry, 36, 6424-6436. PubMed id: 9174359 DOI: 10.1021/bi970085p
Date:
14-Mar-97     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03036  (RCRO_BP434) -  Regulatory protein cro
Seq:
Struc:
71 a.a.
71 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: 10.1021/bi970085p Biochemistry 36:6424-6436 (1997)
PubMed id: 9174359  
 
 
Three-dimensional solution structure and stability of phage 434 Cro protein.
S.Padmanabhan, M.A.Jiménez, C.Gonzalez, J.M.Sanz, G.Giménez-Gallego, M.Rico.
 
  ABSTRACT  
 
1H NMR resonances of the phage 434 Cro protein were assigned using standard 2D NMR methods, and its solution structure determined using 867 distance constraints in distance geometry (DIANA) calculations ultimately refined by restrained molecular dynamics (GROMOS). In the 20 best NMR structures, the average pairwise backbone and heavy atom RMSDs are 0.63 +/- 0.14 and 1.53 +/- 0.15 A, respectively, for the structurally well-defined residues 4-65. Residues 1-3 and 66-71 at the N- and C-termini are structurally disordered. The region 4-65 includes five alpha-helices and tight turns which define the hydrophobic core of the protein. The backbone and heavy atom RMSDs for residues 4-65 are 0.92 +/- 0.12 and 1.99 +/- 0.12 A, respectively, for the NMR versus the crystal structures, but there are significant differences in the side-chain conformations and solvent accessibilities for some core residues. Analytical ultracentrifugation experiments confirm that 434 Cro is monomeric even at the high NMR concentrations. 434 Cro folding under NMR solution conditions is two-state as indicated by coincident urea denaturation curves from circular dichroism and intrinsic fluorescence measurements. They yield values for 434 Cro stability which show good correspondence to the free energy for global unfolding determined by NMR hydrogen exchange measurements for the slowest exchanging amide protons.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16820531 M.van Dijk, A.D.van Dijk, V.Hsu, R.Boelens, and A.M.Bonvin (2006).
Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility.
  Nucleic Acids Res, 34, 3317-3325.  
14997471 H.Sasaki, K.Ikeda, M.Suzuki, K.Ninomiya, and M.Sisido (2004).
Incorporation of anthraquinonyl group into lambda-Cro repressor protein for strand- and position-specific photocleavage of double-stranded DNA.
  Biopolymers, 76, 21-26.  
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
12557184 C.González, J.L.Neira, S.Ventura, S.Bronsoms, M.Rico, and F.X.Avilés (2003).
Structure and dynamics of the potato carboxypeptidase inhibitor by 1H and 15N NMR.
  Proteins, 50, 410-422.
PDB code: 1h20
12511493 K.Fromknecht, P.D.Vogel, and J.G.Wise (2003).
Combinatorial redesign of the DNA binding specificity of a prokaryotic helix-turn-helix repressor.
  J Bacteriol, 185, 475-481.  
12644502 K.M.Jones, W.J.Buikema, and R.Haselkorn (2003).
Heterocyst-specific expression of patB, a gene required for nitrogen fixation in Anabaena sp. strain PCC 7120.
  J Bacteriol, 185, 2306-2314.  
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.  
11980478 F.N.Barrera, M.T.Garzón, J.Gómez, and J.L.Neira (2002).
Equilibrium unfolding of the C-terminal SAM domain of p73.
  Biochemistry, 41, 5743-5753.  
11076539 D.V.Laurents, S.Corrales, M.Elías-Arnanz, P.Sevilla, M.Rico, and S.Padmanabhan (2000).
Folding kinetics of phage 434 Cro protein.
  Biochemistry, 39, 13963-13973.  
  10452612 S.Padmanabhan, M.A.Jiménez, and M.Rico (1999).
Folding propensities of synthetic peptide fragments covering the entire sequence of phage 434 Cro protein.
  Protein Sci, 8, 1675-1688.  
9519304 J.Clarke, and L.S.Itzhaki (1998).
Hydrogen exchange and protein folding.
  Curr Opin Struct Biol, 8, 112-118.  
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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