6NXV

Crystal structure of the theta class glutathione S-transferase from the citrus canker pathogen Xanthomonas axonopodis pv. citri, apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history


Literature

Structural and biochemical characterization of a glutathione transferase from the citrus canker pathogen Xanthomonas.

Hilario, E.De Keyser, S.Fan, L.

(2020) Acta Crystallogr D Struct Biol 76: 778-789

  • DOI: https://doi.org/10.1107/S2059798320009274
  • Primary Citation of Related Structures:  
    6NV6, 6NXV

  • PubMed Abstract: 

    The genus Xanthomonas comprises several cosmopolitan plant-pathogenic bacteria that affect more than 400 plant species, most of which are of economic interest. Citrus canker is a bacterial disease that affects citrus species, reducing fruit yield and quality, and is caused by the bacterium Xanthomonas citri subsp. citri (Xac). The Xac3819 gene, which has previously been reported to be important for citrus canker infection, encodes an uncharacterized glutathione S-transferase (GST) of 207 amino-acid residues in length (XacGST). Bacterial GSTs are implicated in a variety of metabolic processes such as protection against chemical and oxidative stresses. XacGST shares high sequence identity (45%) with the GstB dehalogenase from Escherichia coli O6:H1 strain CFT073 (EcGstB). Here, XacGST is reported to be able to conjugate glutathione (GSH) with bromoacetate with a K m of 6.67 ± 0.77 mM, a k cat of 42.69 ± 0.32 s -1 and a k cat /K m of 6.40 ± 0.72 mM -1  s -1 under a saturated GSH concentration (3.6 mM). These values are comparable to those previously reported for EcGstB. In addition, crystal structures of XacGST were determined in the apo form (PDB entry 6nxv) and in a GSH-bound complex (PDB entry 6nv6). XacGST has a canonical GST-like fold with a conserved serine residue (Ser12) at the GSH-binding site near the N-terminus, indicating XacGST to be a serine-type GST that probably belongs to the theta-class GSTs. GSH binding stabilizes a loop of about 20 residues containing a helix that is disordered in the apo XacGST structure.


  • Organizational Affiliation

    Department of Biochemistry, University of California-Riverside, Riverside, California, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase
A, B, C, D
207Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: gstXAC3819
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download Ideal Coordinates CCD File 
K [auth B],
P [auth C],
Q [auth C],
R [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.159α = 90
b = 105.5β = 90
c = 124.32γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
SCALAdata scaling
PHASERphasing
DMphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institute of Food and Agriculture (NIFA, United States)United StatesCA-R-BCH-5051-H

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description