2Q2K

Structure of nucleic-acid binding protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

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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: https://doi.org/10.1038/nature06392
  • Primary Citation of Related Structures:  
    2Q2K

  • 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. The centromeres of partition (par) systems typically consist of a tandem arrangement of direct repeats ...

    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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical proteinB [auth A],
C [auth B]		70Staphylococcus aureusMutation(s): 0 
Gene Names: 
UniProt
Find proteins for O87365 (Staphylococcus aureus)
Explore O87365 
Go to UniProtKB:  O87365
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87365
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
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')A [auth F]20N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
D [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.3α = 90
b = 56.3β = 90
c = 232.5γ = 120
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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