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PDBsum entry 1zs4

Go to PDB code: 
protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1zs4
Jmol
Contents
Protein chains
82 a.a. *
73 a.a. *
DNA/RNA
Waters ×417
* Residue conservation analysis
PDB id:
1zs4
Name: Transcription/DNA
Title: Structure of bacteriophage lambda cii protein in complex wit
Structure: DNA - 27mer. Chain: u. Engineered: yes. DNA - 27mer. Chain: t. Engineered: yes. Regulatory protein cii. Chain: a, b, c, d. Engineered: yes
Source: Synthetic: yes. Other_details: synthetic. Enterobacteria phage lambda. Organism_taxid: 10710. Gene: cii. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PQS)
Resolution:
1.70Å     R-factor:   0.209     R-free:   0.228
Authors: D.Jain,Y.Kim,K.L.Maxwell,S.Beasley,G.N.Gussin,A.M.Edwards,S.
Key ref:
D.Jain et al. (2005). Crystal structure of bacteriophage lambda cII and its DNA complex. Mol Cell, 19, 259-269. PubMed id: 16039594 DOI: 10.1016/j.molcel.2005.06.006
Date:
23-May-05     Release date:   23-Aug-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03042  (RPC2_LAMBD) -  Transcriptional activator II
Seq:
Struc:
97 a.a.
82 a.a.*
Protein chain
Pfam   ArchSchema ?
P03042  (RPC2_LAMBD) -  Transcriptional activator II
Seq:
Struc:
97 a.a.
73 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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

 

 
DOI no: 10.1016/j.molcel.2005.06.006 Mol Cell 19:259-269 (2005)
PubMed id: 16039594  
 
 
Crystal structure of bacteriophage lambda cII and its DNA complex.
D.Jain, Y.Kim, K.L.Maxwell, S.Beasley, R.Zhang, G.N.Gussin, A.M.Edwards, S.A.Darst.
 
  ABSTRACT  
 
The tetrameric cII protein from bacteriophage lambda activates transcription from the phage promoters P(RE), P(I), and P(AQ) by binding to two direct repeats that flank the promoter -35 element. Here, we present the X-ray crystal structure of cII alone (2.8 A resolution) and in complex with its DNA operator from P(RE) (1.7 A resolution). The structures provide a basis for modeling of the activation complex with the RNA polymerase holoenzyme, and point to the key role for the RNA polymerase alpha subunit C-terminal domain (alphaCTD) in cII-dependent activation, which forms a bridge of protein/protein interactions between cII and the RNA polymerase sigma subunit. The model makes specific predictions for protein/protein interactions between cII and alphaCTD, and between alphaCTD and sigma, which are supported by previous genetic studies.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. λcII Monomer Conformations
Figure 4.
Figure 4. Schematic of λcII/DNA Contacts
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 19, 259-269) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19776236 P.K.Parua, A.B.Datta, and P.Parrack (2010).
Specific hydrophobic residues in the alpha4 helix of lambdaCII are crucial for maintaining its tetrameric structure and directing the lysogenic choice.
  J Gen Virol, 91, 306-312.  
20639540 T.Massad, K.Skaar, H.Nilsson, P.Damberg, P.Henriksson-Peltola, E.Haggård-Ljungquist, M.Högbom, and P.Stenmark (2010).
Crystal structure of the P2 C-repressor: a binder of non-palindromic direct DNA repeats.
  Nucleic Acids Res, 38, 7778-7790.
PDB code: 2xcj
19666711 H.H.Kimsey, and M.K.Waldor (2009).
Vibrio cholerae LexA coordinates CTX prophage gene expression.
  J Bacteriol, 191, 6788-6795.  
18644840 J.E.McGeehan, S.D.Streeter, S.J.Thresh, N.Ball, R.B.Ravelli, and G.G.Kneale (2008).
Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
  Nucleic Acids Res, 36, 4778-4787.
PDB code: 3clc
19091116 R.Villafane, M.Zayas, E.B.Gilcrease, A.M.Kropinski, and S.R.Casjens (2008).
Genomic analysis of bacteriophage epsilon34 of Salmonella enterica serovar Anatum (15+).
  BMC Microbiol, 8, 227.  
17554050 K.L.Maxwell, and L.Frappier (2007).
Viral proteomics.
  Microbiol Mol Biol Rev, 71, 398-411.  
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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