2NRA

Crystal structure of Pi initiator protein in complex with iteron DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication.

Swan, M.K.Bastia, D.Davies, C.

(2006) Proc.Natl.Acad.Sci.Usa 103: 18481-18486

  • DOI: 10.1073/pnas.0609046103

  • PubMed Abstract: 
  • We have determined the crystal structure of a monomeric biologically active form of the pi initiator protein of plasmid R6K as a complex with a single copy of its cognate DNA-binding site (iteron) at 3.1-A resolution. The initiator belongs to the fam ...

    We have determined the crystal structure of a monomeric biologically active form of the pi initiator protein of plasmid R6K as a complex with a single copy of its cognate DNA-binding site (iteron) at 3.1-A resolution. The initiator belongs to the family of winged helix type of proteins. The structure reveals that the protein contacts the iteron DNA at two primary recognition helices, namely the C-terminal alpha4' and the N-terminal alpha4 helices, that recognize the 5' half and the 3' half of the 22-bp iteron, respectively. The base-amino acid contacts are all located in alpha4', whereas the alpha4 helix and its vicinity mainly contact the phosphate groups of the iteron. Mutational analyses show that the contacts of both recognition helices with DNA are necessary for iteron binding and replication initiation. Considerations of a large number of site-directed mutations reveal that two distinct regions, namely alpha2 and alpha5 and its vicinity, are required for DNA looping and initiator dimerization, respectively. Further analysis of mutant forms of pi revealed the possible domain that interacts with the DnaB helicase. Thus, the structure-function analysis presented illuminates aspects of initiation mechanism of R6K and its control.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PI protein
C
276Escherichia coliMutation(s): 4 
Gene Names: pir
Find proteins for P03067 (Escherichia coli)
Go to UniProtKB:  P03067
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*AP*AP*CP*AP*TP*GP*AP*GP*AP*GP*CP*TP*TP*AP*GP*TP*AP*CP*GP*TP*CP*T)-3'A23N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*GP*TP*AP*CP*TP*AP*AP*GP*CP*TP*CP*TP*CP*AP*TP*GP*TP*TP*CP*T)-3'B23N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 125.900α = 90.00
b = 125.900β = 90.00
c = 138.200γ = 120.00
Software Package:
Software NamePurpose
SERGUIdata collection
SOLVEphasing
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance