Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 23.11 kDa 
• Atom Count: 1619 
• Modelled Residue Count: 191 
• Deposited Residue Count: 204 
• Unique protein chains: 1

1UPG

Crystal structure of the quorum-sensing protein TraM from Agrobacterium tumefaciens

• PDB DOI: 10.2210/pdb1UPG/pdb

• Classification: TRANSCRIPTION REPRESSOR
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-30 Released: 2004-05-25 
• Deposition Author(s): Vannini, A., Di Marco, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Crystal Structure of the Quorum-Sensing Protein Tram and its Interaction with the Transcriptional Regulator Trar

Vannini, A., Volpari, C., Di Marco, S.

(2004) J Biol Chem 279: 24291

• PubMed: 15044488 
• DOI: 10.1074/jbc.M401855200
• Primary Citation of Related Structures:  
  1UPG, 1US6


• PubMed Abstract: 
  

Transfer of the tumor-inducing plasmid in Agrobacterium tumefaciens is controlled by a quorum-sensing system whose main components are the transcriptional regulator TraR and its autoinducer. This system allows bacteria to synchronize infection of the host plant when a "quorum" of cells has been reached. TraM is an A. tumefaciens protein involved in the regulation of this system because it binds to TraR and prevents it from binding DNA. As a first step to understanding the molecular basis for the regulation of TraR by TraM, we have determined the crystal structure of TraM at 1.65 A resolution. This protein is packed as a dimer, with each monomer consisting mainly of two antiparallel alpha helices. Monomers are tightly associated, with a large hydrophobic area buried upon dimerization. Secondly, we characterized the TraR-TraM complex in vitro. TraM (11.4 kDa, monomer molecular mass) binds tightly TraR (27 kDa, monomer molecular mass) forming a stable oligomeric complex that likely accounts for two TraR and two TraM dimers.

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Organizational Affiliation: 

Department of Biochemistry, Istituto di Ricerche di Biologia Molecolare Pietro Angeletti, 00040 Pomezia, Rome, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTIONAL REPRESSOR TRAM	A, B	102	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: traM
UniProt
Find proteins for Q57471 (Rhizobium radiobacter) Explore Q57471  Go to UniProtKB:  Q57471

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.436	α = 90
b = 47.097	β = 90
c = 47.469	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-30 
• Released Date: 2004-05-25 
Deposition Author(s): Vannini, A., Di Marco, S.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance