2Q2K

Structure of nucleic-acid binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Segrosome structure revealed by a complex of ParR with centromere DNA.

Schumacher, M.A.Glover, T.C.Brzoska, A.J.Jensen, S.O.Dunham, T.D.Skurray, R.A.Firth, N.

(2007) Nature 450: 1268-1271

  • DOI: 10.1038/nature06392

  • PubMed Abstract: 
  • The stable inheritance of genetic material depends on accurate DNA partition. Plasmids serve as tractable model systems to study DNA segregation because they require only a DNA centromere, a centromere-binding protein and a force-generating ATPase. T ...

    The stable inheritance of genetic material depends on accurate DNA partition. Plasmids serve as tractable model systems to study DNA segregation because they require only a DNA centromere, a centromere-binding protein and a force-generating ATPase. The centromeres of partition (par) systems typically consist of a tandem arrangement of direct repeats. The best-characterized par system contains a centromere-binding protein called ParR and an ATPase called ParM. In the first step of segregation, multiple ParR proteins interact with the centromere repeats to form a large nucleoprotein complex of unknown structure called the segrosome, which binds ParM filaments. pSK41 ParR binds a centromere consisting of multiple 20-base-pair (bp) tandem repeats to mediate both transcription autoregulation and segregation. Here we report the structure of the pSK41 segrosome revealed in the crystal structure of a ParR-DNA complex. In the crystals, the 20-mer tandem repeats stack pseudo-continuously to generate the full-length centromere with the ribbon-helix-helix (RHH) fold of ParR binding successive DNA repeats as dimer-of-dimers. Remarkably, the dimer-of-dimers assemble in a continuous protein super-helical array, wrapping the DNA about its positive convex surface to form a large segrosome with an open, solenoid-shaped structure, suggesting a mechanism for ParM capture and subsequent plasmid segregation.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas, M.D. Anderson Cancer Center, Unit 1000, Houston, TX 77030, USA. maschuma@mdanderson.org




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein
A, B
70Staphylococcus aureusMutation(s): 0 
Gene Names: parR
Find proteins for O87365 (Staphylococcus aureus)
Go to UniProtKB:  O87365
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*TP*AP*TP*AP*(5IU)P*AP*CP*(5IU)P*AP*GP*TP*AP*TP*AP*TP*AP*CP*T)-3')F20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
F
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.258 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.300α = 90.00
b = 56.300β = 90.00
c = 232.500γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
SCALAdata scaling
ADSCdata collection
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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