2FD4

Crystal Structure of AvrPtoB (436-553)

• PDB DOI: https://doi.org/10.2210/pdb2FD4/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas syringae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-13 Released: 2005-12-27 
• Deposition Author(s): Janjusevic, R., Stebbins, C.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Literature

A bacterial inhibitor of host programmed cell death defenses is an E3 ubiquitin ligase.

Janjusevic, R., Abramovitch, R.B., Martin, G.B., Stebbins, C.E.

(2006) Science 311: 222-226

• PubMed: 16373536 
• DOI: https://doi.org/10.1126/science.1120131
• Primary Citation of Related Structures:  
  2FD4


• PubMed Abstract: 
  

  The Pseudomonas syringae protein AvrPtoB is translocated into plant cells, where it inhibits immunity-associated programmed cell death (PCD). The structure of a C-terminal domain of AvrPtoB that is essential for anti-PCD activity reveals an unexpected homology to the U-box and RING-finger components of eukaryotic E3 ubiquitin ligases, and we show that AvrPtoB has ubiquitin ligase activity. Mutation of conserved residues involved in the binding of E2 ubiquitin-conjugating enzymes abolishes this activity in vitro, as well as anti-PCD activity in tomato leaves, which dramatically decreases virulence. These results show that Pseudomonas syringae uses a mimic of host E3 ubiquitin ligases to inactivate plant defenses.

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Organizational Affiliation: 

Laboratory of Structural Microbiology, Rockefeller University, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.29 kDa 
• Atom Count: 852 
• Modelled Residue Count: 105 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
avirulence protein AvrptoB	A	122	Pseudomonas syringae	Mutation(s): 0  EC: 2.3.2
UniProt
Find proteins for Q8RSY1 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q8RSY1  Go to UniProtKB:  Q8RSY1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.863	α = 90
b = 61.863	β = 90
c = 60.419	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-27 
Deposition Author(s): Janjusevic, R., Stebbins, C.E.

Revision History  

• Version 1.0: 2005-12-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references