2OIV | pdb_00002oiv

Structural Analysis of Xanthomonas XopD Provides Insights Into Substrate Specificity of Ubiquitin-like Protein Proteases

• PDB DOI: https://doi.org/10.2210/pdb2OIV/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas euvesicatoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-11 Released: 2007-05-29 
• Deposition Author(s): Chosed, R., Tomchick, D.R., Brautigam, C.A., Machius, M., Orth, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.250 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Structural analysis of Xanthomonas XopD provides insights into substrate specificity of ubiquitin-like protein proteases.

Chosed, R., Tomchick, D.R., Brautigam, C.A., Mukherjee, S., Negi, V.S., Machius, M., Orth, K.

(2007) J Biological Chem 282: 6773-6782

• PubMed: 17204475 
• DOI: https://doi.org/10.1074/jbc.M608730200
• Primary Citation Related Structures: 
  2OIV, 2OIX


• PubMed Abstract: 
  

  XopD (Xanthomonas outer protein D), a type III secreted effector from Xanthomonas campestris pv. vesicatoria, is a desumoylating enzyme with strict specificity for its plant small ubiquitin-like modifier (SUMO) substrates. Based on SUMO sequence alignments and peptidase assays with various plant, yeast, and mammalian SUMOs, we identified residues in SUMO that contribute to XopD/SUMO recognition. Further predictions regarding the enzyme/substrate specificity were made by solving the XopD crystal structure. By incorporating structural information with sequence alignments and enzyme assays, we were able to elucidate determinants of the rigid SUMO specificity exhibited by the Xanthomonas virulence factor XopD.

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Organizational Affiliation: 
• Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.86 kDa 
• Atom Count: 1,438 
• Modeled Residue Count: 170 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthomonas outer protein D	A	186	Xanthomonas euvesicatoria	Mutation(s): 0  Gene Names: xopD
UniProt
Find proteins for Q3BYJ5 (Xanthomonas euvesicatoria pv. vesicatoria (strain 85-10)) Explore Q3BYJ5  Go to UniProtKB:  Q3BYJ5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.250 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.618	α = 90
b = 91.618	β = 90
c = 44.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Chosed, R., Tomchick, D.R., Brautigam, C.A., Machius, M., Orth, K.

Revision History  

• Version 1.0: 2007-05-29
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations