3ON0

Crystal structure of the pED208 TraM-sbmA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.874 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of cooperative DNA recognition by the plasmid conjugation factor, TraM.

Wong, J.J.Lu, J.Edwards, R.A.Frost, L.S.Glover, J.N.

(2011) Nucleic Acids Res. 39: 6775-6788

  • DOI: 10.1093/nar/gkr296
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The conjugative transfer of F-like plasmids such as F, R1, R100 and pED208, between bacterial cells requires TraM, a plasmid-encoded DNA-binding protein. TraM tetramers bridge the origin of transfer (oriT) to a key component of the conjugative pore, ...

    The conjugative transfer of F-like plasmids such as F, R1, R100 and pED208, between bacterial cells requires TraM, a plasmid-encoded DNA-binding protein. TraM tetramers bridge the origin of transfer (oriT) to a key component of the conjugative pore, the coupling protein TraD. Here we show that TraM recognizes a high-affinity DNA-binding site, sbmA, as a cooperative dimer of tetramers. The crystal structure of the TraM-sbmA complex from the plasmid pED208 shows that binding cooperativity is mediated by DNA kinking and unwinding, without any direct contact between tetramers. Sequence-specific DNA recognition is carried out by TraM's N-terminal ribbon-helix-helix (RHH) domains, which bind DNA in a staggered arrangement. We demonstrate that both DNA-binding specificity, as well as selective interactions between TraM and the C-terminal tail of its cognate TraD mediate conjugation specificity within the F-like family of plasmids. The ability of TraM to cooperatively bind DNA without interaction between tetramers leaves the C-terminal TraM tetramerization domains free to make multiple interactions with TraD, driving recruitment of the plasmid to the conjugative pore.


    Organizational Affiliation

    Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein traM
A, B, C, D
127Escherichia coliMutation(s): 0 
Gene Names: traM
Find proteins for P33788 (Escherichia coli)
Go to UniProtKB:  P33788
Entity ID: 2
MoleculeChainsLengthOrganism
sbmAP24N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.874 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.250 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 93.025α = 90.00
b = 154.687β = 90.00
c = 167.565γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-09-07
    Type: Database references