Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.39 kDa 
• Atom Count: 1605 
• Residue Count: 188 
• Unique protein chains: 1

1UKF

Crystal Structure of Pseudomonas Avirulence Protein AvrPphB

• DOI: 10.2210/pdb1UKF/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas savastanoi pv. phaseolicola
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-08-21 Released: 2003-12-09 
• Deposition Author(s): Zhu, M., Shao, F., Innes, R.W., Dixon, J.E., Xu, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.222 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Literature

The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site.

Zhu, M., Shao, F., Innes, R.W., Dixon, J.E., Xu, Z.

(2004) Proc Natl Acad Sci U S A 101: 302-307

• PubMed: 14694194 
• DOI: 10.1073/pnas.2036536100
• Primary Citation of Related Structures:  
  1UKF


• PubMed Abstract: 
  

AvrPphB is an avirulence (Avr) protein from the plant pathogen Pseudomonas syringae that can trigger a disease-resistance response in a number of host plants including Arabidopsis. AvrPphB belongs to a novel family of cysteine proteases with the charter member of this family being the Yersinia effector protein YopT. AvrPphB has a very stringent substrate specificity, catalyzing a single proteolytic cleavage in the Arabidopsis serine/threonine kinase PBS1. We have determined the crystal structure of AvrPphB by x-ray crystallography at 1.35-A resolution. The structure is composed of a central antiparallel beta-sheet, with alpha-helices packing on both sides of the sheet to form a two-lobe structure. The core of this structure resembles the papain-like cysteine proteases. The similarity includes the AvrPphB active site catalytic triad of Cys-98, His-212, and Asp-227 and the oxyanion hole residue Asn-93. Based on analogy with inhibitor complexes of the papain-like proteases, we propose a model for the substrate-binding mechanism of AvrPphB. A deep and positively charged pocket (S2) and a neighboring shallow surface (S3) likely bind to aspartic acid and glycine residues in the substrate located two (P2) and three (P3) residues N terminal to the cleavage site, respectively. Further implications about the specificity of plant pathogen recognition are also discussed.

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Organizational Affiliation: 

Department of Biological Chemistry, Medical School and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avirulence protein AVRPPH3	A	188	Pseudomonas savastanoi pv. phaseolicola	Mutation(s): 0  Gene Names: avrPph3 EC: 3.4.22
Find proteins for Q52430 (Pseudomonas savastanoi pv. phaseolicola) Explore Q52430  Go to UniProtKB:  Q52430

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.222 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.601	α = 90
b = 49.596	β = 90
c = 75.705	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-21 
• Released Date: 2003-12-09 
Deposition Author(s): Zhu, M., Shao, F., Innes, R.W., Dixon, J.E., Xu, Z.

Revision History 

• Version 1.0: 2003-12-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance