2R1J

Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

P22 c2 repressor-operator complex: mechanisms of direct and indirect readout

Watkins, D.Hsiao, C.Woods, K.K.Koudelka, G.B.Williams, L.D.

(2008) Biochemistry 47: 2325-2338

  • DOI: 10.1021/bi701826f

  • PubMed Abstract: 
  • The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps to direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. We describe the 1.6 A X-ray structure of the N-terminal domain (NTD) of P22R i ...

    The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps to direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. We describe the 1.6 A X-ray structure of the N-terminal domain (NTD) of P22R in a complex with a DNA fragment containing the synthetic operator sequence [d(ATTTAAGATATCTTAAAT)]2. This operator has an A-T base pair at position 9L and a T-A base pair at position 9R and is termed DNA9T. Direct readout: nondirectional van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD-DNA9T complex suggests that sequence-specificity arises substantially from lock-and-key interaction of a valine with a complementary binding cleft on the major groove surface of DNA9T. The cleft is formed by four methyl groups on sequential base pairs of 5'-TTAA-3'. The valine cleft is intrinsic to the DNA sequence and does not arise from protein-induced DNA conformational changes. Protein-DNA hydrogen bonding plays a secondary role in specificity. Indirect readout: it is known that the noncontacted bases in the center of the complex are important determinants of affinity. The protein induces a transition of the noncontacted region from B-DNA to B'-DNA. The B' state is characterized by a narrow minor groove and a zigzag spine of hydration. The free energy of the transition from B- to B'-DNA is known to depend on the sequence. Thus, the observed DNA conformation and hydration allows for the formulation of a predictive model of the indirect readout phenomenon.


    Organizational Affiliation

    School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Repressor protein C2
L, R
68Salmonella phage P22Mutation(s): 0 
Gene Names: C2
Find proteins for P69202 (Salmonella phage P22)
Go to Gene View: C2
Go to UniProtKB:  P69202
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*DCP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DA)-3'B20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*DTP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DG)-3'A20N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.204 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 64.105α = 90.00
b = 64.105β = 90.00
c = 101.685γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description