2G7O

Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM.

Lu, J.Edwards, R.A.Wong, J.J.Manchak, J.Scott, P.G.Frost, L.S.Glover, J.N.

(2006) Embo J. 25: 2930-2939

  • DOI: 10.1038/sj.emboj.7601151
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • TraM is essential for F plasmid-mediated bacterial conjugation, where it binds to the plasmid DNA near the origin of transfer, and recognizes a component of the transmembrane DNA transfer complex, TraD. Here we report the 1.40 A crystal structure of ...

    TraM is essential for F plasmid-mediated bacterial conjugation, where it binds to the plasmid DNA near the origin of transfer, and recognizes a component of the transmembrane DNA transfer complex, TraD. Here we report the 1.40 A crystal structure of the TraM core tetramer (TraM58-127). TraM58-127 is a compact eight-helical bundle, in which the N-terminal helices from each protomer interact to form a central, parallel four-stranded coiled-coil, whereas each C-terminal helix packs in an antiparallel arrangement around the outside of the structure. Four protonated glutamic acid residues (Glu88) are packed in a hydrogen-bonded arrangement within the central four-helix bundle. Mutational and biophysical analyses indicate that this protonated state is in equilibrium with a deprotonated tetrameric form characterized by a lower helical content at physiological pH and temperature. Comparison of TraM to its Glu88 mutants predicted to stabilize the helical structure suggests that the protonated state is the active form for binding TraD in conjugation.


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein traM
A
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: traM
Find proteins for P10026 (Escherichia coli (strain K12))
Go to UniProtKB:  P10026
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.193 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 51.733α = 90.00
b = 51.733β = 90.00
c = 49.585γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
RESOLVEphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description