Crystal structure of a second quorum sensing antiactivator TraM2 from A. tumefaciens strain A6

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.229 

Starting Model: experimental
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Crystal Structure and Mechanism of TraM2, a Second Quorum-Sensing Antiactivator of Agrobacterium tumefaciens Strain A6.

Chen, G.Wang, C.Fuqua, C.Zhang, L.H.Chen, L.

(2006) J Bacteriol 188: 8244-8251

  • DOI: https://doi.org/10.1128/JB.00954-06
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Quorum sensing is a community behavior that bacteria utilize to coordinate a variety of population density-dependent biological functions. In Agrobacterium tumefaciens, quorum sensing regulates the replication and conjugative transfer of the tumor-inducing (Ti) plasmid from pathogenic strains to nonpathogenic derivatives. Most of the quorum-sensing regulatory proteins are encoded within the Ti plasmid. Among these, TraR is a LuxR-type transcription factor playing a key role as the quorum-sensing signal receptor, and TraM is an antiactivator that antagonizes TraR through the formation of a stable oligomeric complex. Recently, a second TraM homologue called TraM2, not encoded on the Ti plasmid of A. tumefaciens A6, was identified, in addition to a copy on the Ti plasmid. In this report, we have characterized TraM2 and its interaction with TraR and solved its crystal structure to 2.1 A. Like TraM, TraM2 folds into a helical bundle and exists as homodimer. TraM2 forms a stable complex (K(d) = 8.6 nM) with TraR in a 1:1 binding ratio, a weaker affinity than that of TraM for TraR. Structural analysis and biochemical studies suggest that protein stability may account for the difference between TraM2 and TraM in their binding affinities to TraR and provide a structural basis for L54 in promoting structural stability of TraM.

  • Organizational Affiliation

    Department of Biology, 915 E. 3rd St., Indiana University, Bloomington, Indiana 47405, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Quorum-sensing antiactivator
A, B, C, D
102Agrobacterium tumefaciensMutation(s): 0 
Gene Names: traM2
Find proteins for Q20HX4 (Rhizobium radiobacter)
Explore Q20HX4 
Go to UniProtKB:  Q20HX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ20HX4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.229 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.521α = 90
b = 79.521β = 90
c = 90.238γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2006-10-31 
  • Deposition Author(s): Chen, L.

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-31
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description