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PDBsum entry 2gdr

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2gdr
Jmol
Contents
Protein chains
(+ 0 more) 202 a.a. *
Ligands
GSH ×9
Waters ×215
* Residue conservation analysis
PDB id:
2gdr
Name: Transferase
Title: Crystal structure of a bacterial glutathione transferase
Structure: Glutathione s-transferase. Chain: a, b, c, d, e, f. Engineered: yes
Source: Burkholderia xenovorans. Organism_taxid: 266265. Strain: lb400. Gene: bphk. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.161     R-free:   0.204
Authors: E.I.Tocheva,P.D.Fortin,L.D.Eltis,M.E.P.Murphy
Key ref:
E.I.Tocheva et al. (2006). Structures of ternary complexes of BphK, a bacterial glutathione S-transferase that reductively dechlorinates polychlorinated biphenyl metabolites. J Biol Chem, 281, 30933-30940. PubMed id: 16920719 DOI: 10.1074/jbc.M603125200
Date:
16-Mar-06     Release date:   22-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q59721  (Q59721_BURXL) -  Glutathione S-transferase
Seq:
Struc:
203 a.a.
202 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.5.1.18  - Glutathione transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RX + glutathione = HX + R-S-glutathione
RX
+
glutathione
Bound ligand (Het Group name = GSH)
corresponds exactly
= HX
+ R-S-glutathione
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     transferase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M603125200 J Biol Chem 281:30933-30940 (2006)
PubMed id: 16920719  
 
 
Structures of ternary complexes of BphK, a bacterial glutathione S-transferase that reductively dechlorinates polychlorinated biphenyl metabolites.
E.I.Tocheva, P.D.Fortin, L.D.Eltis, M.E.Murphy.
 
  ABSTRACT  
 
Prokaryotic glutathione S-transferases are as diverse as their eukaryotic counterparts but are much less well characterized. BphK from Burkholderia xenovorans LB400 consumes two GSH molecules to reductively dehalogenate chlorinated 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), inhibitory polychlorinated biphenyl metabolites. Crystallographic structures of two ternary complexes of BphK were solved to a resolution of 2.1A. In the BphK-GSH-HOPDA complex, GSH and HOPDA molecules occupy the G- and H-subsites, respectively. The thiol nucleophile of the GSH molecule is positioned for SN2 attack at carbon 3 of the bound HOPDA. The respective sulfur atoms of conserved Cys-10 and the bound GSH are within 3.0A, consistent with product release and the formation of a mixed disulfide intermediate. In the BphK-(GSH)2 complex, a GSH molecule occupies each of the two subsites. The three sulfur atoms of the two GSH molecules and Cys-10 are aligned suitably for a disulfide exchange reaction that would regenerate the resting enzyme and yield disulfide-linked GSH molecules. A second conserved residue, His-106, is adjacent to the thiols of Cys-10 and the GSH bound to the G-subsite and thus may stabilize a transition state in the disulfide exchange reaction. Overall, the structures support and elaborate a proposed dehalogenation mechanism for BphK and provide insight into the plasticity of the H-subsite.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. The active sites of the BphK-GSH-HOPDA ternary complex (A) and the BphK-(GSH)[2] ternary complex (B). Residues comprising the active site, the bound HOPDA, and the GSH molecules are shown as ball-and-stick models. Carbon atoms are colored yellow (GSH and HOPDA) and orange (amino acid side chains), nitrogen atoms are colored blue, oxygen atoms are colored red, and sulfur atoms are colored green. Secondary structures of the two monomers comprising a homodimer are colored in cyan and slate. Average distances are indicated beside dotted lines. C, stereo image of the superposition of the active sites of the BphK-GSH-HOPDA and the BphK-(GSH)[2] complexes. Side chain carbon atoms from the BphK-GSH-HOPDA complex are colored beige, and the GSH and HOPDA carbon atoms are colored yellow. Side chain carbon atoms from the BphK-(GSH)[2] complex are colored orange, and the carbon atoms of the two GSH molecules are colored cyan. In both structures, oxygen atoms are colored red, nitrogen atoms are colored blue, and sulfur atoms are colored magenta.
Figure 3.
FIGURE 3. Proposed mechanism for the BphK-catalyzed reductive dehalogenation of 3-Cl HOPDA. The first half-reaction involves tautomerization of the HOPDA molecule followed by nucleophilic substitution to form a mixed disulfide. The second half-reaction is a disulfide exchange. Crystallographic data suggest that His-106 stabilizes the negative charge on Cys-10. Enz, enzyme.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 30933-30940) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21428697 A.Oakley (2011).
Glutathione transferases: a structural perspective.
  Drug Metab Rev, 43, 138-151.  
  21425927 S.M.Belchik, and L.Xun (2011).
S-glutathionyl-(chloro)hydroquinone reductases: a new class of glutathione transferases functioning as oxidoreductases.
  Drug Metab Rev, 43, 307-316.  
20663851 L.Federici, M.Masulli, C.Di Ilio, and N.Allocati (2010).
Characterization of the hydrophobic substrate-binding site of the bacterial beta class glutathione transferase from Proteus mirabilis.
  Protein Eng Des Sel, 23, 743-750.  
19194977 G.Emtiazi, T.Saleh, and M.Hassanshahian (2009).
The effect of bacterial glutathione S-transferase on morpholine degradation.
  Biotechnol J, 4, 202-205.  
19016852 N.Allocati, L.Federici, M.Masulli, and C.Di Ilio (2009).
Glutathione transferases in bacteria.
  FEBS J, 276, 58-75.  
18076047 N.Allocati, L.Federici, M.Masulli, B.Favaloro, and C.Di Ilio (2008).
Cysteine 10 is critical for the activity of Ochrobactrum anthropi glutathione transferase and its mutation to alanine causes the preferential binding of glutathione to the H-site.
  Proteins, 71, 16-23.
PDB code: 2pvq
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