3BTP

Crystal structure of Agrobacterium tumefaciens VirE2 in complex with its chaperone VirE1: a novel fold and implications for DNA binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners.

Dym, O.Albeck, S.Unger, T.Jacobovitch, J.Branzburg, A.Michael, Y.Frenkiel-Krispin, D.Wolf, S.G.Elbaum, M.

(2008) Proc.Natl.Acad.Sci.Usa 105: 11170-11175

  • DOI: 10.1073/pnas.0801525105

  • PubMed Abstract: 
  • Agrobacterium tumefaciens infects its plant hosts by a mechanism of horizontal gene transfer. This capability has led to its widespread use in artificial genetic transformation. In addition to DNA, the bacterium delivers an abundant ssDNA binding pro ...

    Agrobacterium tumefaciens infects its plant hosts by a mechanism of horizontal gene transfer. This capability has led to its widespread use in artificial genetic transformation. In addition to DNA, the bacterium delivers an abundant ssDNA binding protein, VirE2, whose roles in the host include protection from cytoplasmic nucleases and adaptation for nuclear import. In Agrobacterium, VirE2 is bound to its acidic chaperone VirE1. When expressed in vitro in the absence of VirE1, VirE2 is prone to oligomerization and forms disordered filamentous aggregates. These filaments adopt an ordered solenoidal form in the presence of ssDNA, which was characterized previously by electron microscopy and three-dimensional image processing. VirE2 coexpressed in vitro with VirE1 forms a soluble heterodimer. VirE1 thus prevents VirE2 oligomerization and competes with its binding to ssDNA. We present here a crystal structure of VirE2 in complex with VirE1, showing that VirE2 is composed of two independent domains presenting a novel fold, joined by a flexible linker. Electrostatic interactions with VirE1 cement the two domains of VirE2 into a locked form. Comparison with the electron microscopy structure indicates that the VirE2 domains adopt different relative orientations. We suggest that the flexible linker between the domains enables VirE2 to accommodate its different binding partners.


    Organizational Affiliation

    Israel Structural Proteomics Center, Chemical Research Support, and Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Single-strand DNA-binding protein
A
556Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Gene Names: virE2
Find proteins for P08062 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  P08062
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein virE1
B
63Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Gene Names: virE1
Find proteins for P08063 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  P08063
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NH4
Query on NH4

Download SDF File 
Download CCD File 
A, B
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.020α = 90.00
b = 96.271β = 90.00
c = 112.483γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXDphasing
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance