2NTZ

Structure of a ParB-DNA complex reveals a double B-box interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.288 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a four-way bridged ParB-DNA complex provides insight into P1 segrosome assembly.

Schumacher, M.A.Mansoor, A.Funnell, B.E.

(2007) J.Biol.Chem. 282: 10456-10464

  • DOI: 10.1074/jbc.M610603200

  • PubMed Abstract: 
  • The plasmid partition process is essential for plasmid propagation and is mediated by par systems, consisting of centromere-like sites and two proteins, ParA and ParB. In the first step of partition by the archetypical P1 system, ParB binds a complic ...

    The plasmid partition process is essential for plasmid propagation and is mediated by par systems, consisting of centromere-like sites and two proteins, ParA and ParB. In the first step of partition by the archetypical P1 system, ParB binds a complicated centromere-like site to form a large nucleoprotein segrosome. ParB is a dimeric DNA-binding protein that can bridge between both A-boxes and B-boxes located on the centromere. Its helix-turn-helix domains bind A-boxes and the dimer domain binds B-boxes. Binding of the first ParB dimer nucleates the remaining ParB molecules onto the centromere site, which somehow leads to the formation of a condensed segrosome superstructure. To further understand this unique DNA spreading capability of ParB, we crystallized and determined the structure of a 1:2 ParB-(142-333):A3-B2-box complex to 3.35A resolution. The structure reveals a remarkable four-way, protein-DNA bridged complex in which both ParB helix-turn-helix domains simultaneously bind adjacent A-boxes and the dimer domain bridges between two B-boxes. The multibridging capability and the novel dimer domain-B-box interaction, which juxtaposes the DNA sites close in space, suggests a mechanism for the formation of the wrapped solenoid-like segrosome superstructure. This multibridging capability of ParB is likely critical in its partition complex formation and pairing functions.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA. maschuma@mdanderson




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ParB
A, B
192Enterobacteria phage P1Gene Names: parB
Find proteins for Q38420 (Enterobacteria phage P1)
Go to UniProtKB:  Q38420
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*GP*AP*AP*AP*TP*CP*GP*CP*CP*AP*CP*GP*A)-3'Y,E16N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*TP*GP*GP*CP*GP*AP*TP*TP*TP*CP*AP*CP*G)-3'W,U16N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.288 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.420α = 90.00
b = 144.420β = 90.00
c = 78.880γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
EPMRphasing
CCP4data scaling
ADSCdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance