3GX0

Crystal Structure of GSH-dependent Disulfide bond Oxidoreductase

• PDB DOI: https://doi.org/10.2210/pdb3GX0/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-01 Released: 2009-07-07 
• Deposition Author(s): Ladner, J.E., Harp, J.M., Wadington, M.C., Armstrong, R.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

Analysis of the structure and function of YfcG from Escherichia coli reveals an efficient and unique disulfide bond reductase.

Wadington, M.C., Ladner, J.E., Stourman, N.V., Harp, J.M., Armstrong, R.N.

(2009) Biochemistry 48: 6559-6561

• PubMed: 19537707 
• DOI: https://doi.org/10.1021/bi9008825
• Primary Citation of Related Structures:  
  3GX0


• PubMed Abstract: 
  

  YfcG is one of eight glutathione (GSH) transferase homologues encoded in the Escherichia coli genome. The protein exhibits low or no GSH transferase activity toward a panel of electrophilic substrates. In contrast, it has a very robust disulfide-bond reductase activity toward 2-hydroxyethyldisulfide on par with mammalian and bacterial glutaredoxins. The structure of YfcG at 2.3 A-resolution from crystals grown in the presence of GSH reveals a molecule of glutathione disulfide in the active site. The crystallographic results and the lack of functional cysteine residues in the active site of YfcG suggests that the reductase activity is unique in that no sulfhydryl groups in the YfcG protein are covalently involved in the redox chemistry.

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Organizational Affiliation: 

Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.16 kDa 
• Atom Count: 1,791 
• Modelled Residue Count: 204 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GST-like protein yfcG	A	215	Escherichia coli K-12	Mutation(s): 0  Gene Names: yfcG
UniProt
Find proteins for P77526 (Escherichia coli (strain K12)) Explore P77526  Go to UniProtKB:  P77526

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDS	B [auth A]	OXIDIZED GLUTATHIONE DISULFIDE C20 H32 N6 O12 S2 YPZRWBKMTBYPTK-BJDJZHNGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GDS	PDBBind:  3GX0	Kd: 3.30e+5 (nM) from 1 assay(s)
	Binding MOAD:  3GX0	Kd: 2400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.49	α = 90
b = 68.49	β = 90
c = 111.99	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Ladner, J.E., Harp, J.M., Wadington, M.C., Armstrong, R.N.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations