3MKZ

Structure of SopB(155-272)-18mer complex, P21 form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes.

Schumacher, M.A.Piro, K.M.Xu, W.

(2010) Nucleic Acids Res. 38: 4514-4526

  • DOI: 10.1093/nar/gkq161
  • Primary Citation of Related Structures:  3KZ5, 3MKW, 3MKY

  • PubMed Abstract: 
  • Accurate DNA segregation is essential for genome transmission. Segregation of the prototypical F plasmid requires the centromere-binding protein SopB, the NTPase SopA and the sopC centromere. SopB displays an intriguing range of DNA-binding propertie ...

    Accurate DNA segregation is essential for genome transmission. Segregation of the prototypical F plasmid requires the centromere-binding protein SopB, the NTPase SopA and the sopC centromere. SopB displays an intriguing range of DNA-binding properties essential for partition; it binds sopC to form a partition complex, which recruits SopA, and it also coats DNA to prevent non-specific SopA-DNA interactions, which inhibits SopA polymerization. To understand the myriad functions of SopB, we determined a series of SopB-DNA crystal structures. SopB does not distort its DNA site and our data suggest that SopB-sopC forms an extended rather than wrapped partition complex with the SopA-interacting domains aligned on one face. SopB is a multidomain protein, which like P1 ParB contains an all-helical DNA-binding domain that is flexibly attached to a compact (beta(3)-alpha)(2) dimer-domain. Unlike P1 ParB, the SopB dimer-domain does not bind DNA. Moreover, SopB contains a unique secondary dimerization motif that bridges between DNA duplexes. Both specific and non-specific SopB-DNA bridging structures were observed. This DNA-linking function suggests a novel mechanism for in trans DNA spreading by SopB, explaining how it might mask DNA to prevent DNA-mediated inhibition of SopA polymerization.


    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: 1
MoleculeChainsSequence LengthOrganismDetails
Protein sopB
A, B, U, N
121Escherichia coli (strain K12)Gene Names: sopB (B)
Find proteins for P62558 (Escherichia coli (strain K12))
Go to UniProtKB:  P62558
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3')C,D,Y,Z18N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, U, Z
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 111.380α = 90.00
b = 47.120β = 115.97
c = 118.230γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-04-15 
  • Released Date: 2010-05-05 
  • Deposition Author(s): Schumacher, M.A.

Revision History 

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance