Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 37.06 kDa 
• Atom Count: 2453 
• Modelled Residue Count: 296 
• Deposited Residue Count: 316 
• Unique protein chains: 1

4NQF

Crystal structure of HEPN domain protein

• DOI: 10.2210/pdb4NQF/pdb

• Classification: TRANSFERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-11-25 Released: 2014-03-26 
• Deposition Author(s): Padavannil, A., Jobichen, C., Sivaraman, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.280 
• R-Value Work: 0.218 
• R-Value Observed: 0.224 

Literature

Dimerization of VirD2 Binding Protein Is Essential for Agrobacterium Induced Tumor Formation in Plants

Padavannil, A., Jobichen, C., Qinghua, Y., Seetharaman, J., Velazquez-campoy, A., Yang, L., Pan, S.Q., Sivaraman, J.

(2014) PLoS Pathog 10: e1003948-e1003948

• PubMed: 24626239 
• DOI: 10.1371/journal.ppat.1003948
• Primary Citation of Related Structures:  
  4NQF


• PubMed Abstract: 
  

The Type IV Secretion System (T4SS) is the only bacterial secretion system known to translocate both DNA and protein substrates. The VirB/D4 system from Agrobacterium tumefaciens is a typical T4SS. It facilitates the bacteria to translocate the VirD2-T-DNA complex to the host cell cytoplasm. In addition to protein-DNA complexes, the VirB/D4 system is also involved in the translocation of several effector proteins, including VirE2, VirE3 and VirF into the host cell cytoplasm. These effector proteins aid in the proper integration of the translocated DNA into the host genome. The VirD2-binding protein (VBP) is a key cytoplasmic protein that recruits the VirD2-T-DNA complex to the VirD4-coupling protein (VirD4 CP) of the VirB/D4 T4SS apparatus. Here, we report the crystal structure and associated functional studies of the C-terminal domain of VBP. This domain mainly consists of α-helices, and the two monomers of the asymmetric unit form a tight dimer. The structural analysis of this domain confirms the presence of a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) fold. Biophysical studies show that VBP is a dimer in solution and that the HEPN domain is the dimerization domain. Based on structural and mutagenesis analyses, we show that substitution of key residues at the interface disrupts the dimerization of both the HEPN domain and full-length VBP. In addition, pull-down analyses show that only dimeric VBP can interact with VirD2 and VirD4 CP. Finally, we show that only Agrobacterium harboring dimeric full-length VBP can induce tumors in plants. This study sheds light on the structural basis of the substrate recruiting function of VBP in the T4SS pathway of A. tumefaciens and in other pathogenic bacteria employing similar systems.

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Organizational Affiliation: 

Department of Biological Sciences, National University of Singapore, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidyltransferase	A, B	158	Agrobacterium fabrum str. C58	Mutation(s): 3  Gene Names: Atu4856
Find proteins for Q7CW19 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CW19  Go to UniProtKB:  Q7CW19

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: 2.70 Å
• R-Value Free: 0.280 
• R-Value Work: 0.218 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.103	α = 90
b = 71.574	β = 90
c = 83.416	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
Phenix-AutoSol	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Phenix-AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-11-25 
• Released Date: 2014-03-26 
Deposition Author(s): Padavannil, A., Jobichen, C., Sivaraman, J.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release