2VCV

Glutathione transferase A3-3 in complex with glutathione and delta-4- androstene-3-17-dione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Featuring of Steroid Isomerase Activity in Alpha Class Glutathione Transferases.

Tars, K.Olin, B.Mannervik, B.

(2010) J Mol Biol 397: 332

  • DOI: 10.1016/j.jmb.2010.01.023
  • Primary Citation of Related Structures:  
    2VCT, 2VCV, 2WJU

  • PubMed Abstract: 
  • Glutathione transferases (GSTs) are abundant enzymes catalyzing the conjugation of hydrophobic toxic substrates with glutathione. In addition to detoxication, human GST A3-3 displays prominent steroid double-bond isomerase activity; e.g. transforming Delta(5)-androstene-3-17-dione into Delta(4)-androstene-3-17-dione (AD) ...

    Glutathione transferases (GSTs) are abundant enzymes catalyzing the conjugation of hydrophobic toxic substrates with glutathione. In addition to detoxication, human GST A3-3 displays prominent steroid double-bond isomerase activity; e.g. transforming Delta(5)-androstene-3-17-dione into Delta(4)-androstene-3-17-dione (AD). This chemical transformation is a crucial step in the biosynthesis of steroids, such as testosterone and progesterone. In contrast to GST A3-3, the homologous GST A2-2 does not show significant steroid isomerase activity. We have solved the 3D structures of human GSTs A2-2 and A3-3 in complex with AD. In the GST A3-3 crystal structure, AD was bound in an orientation suitable for the glutathione (GSH)-mediated catalysis to occur. In GST A2-2, however, AD was bound in a completely different orientation with its reactive double bond distant from the GSH-binding site. The structures illustrate how a few amino acid substitutions in the active site spectacularly alter the binding mode of the steroid substrate in relation to the conserved catalytic groups and an essentially fixed polypeptide chain conformation. Furthermore, AD did not bind to the GST A2-2-GSH complex. Altogether, these results provide a first-time structural insight into the steroid isomerase activity of any GST and explain the 5000-fold difference in catalytic efficiency between GSTs A2-2 and A3-3. More generally, the structures illustrate how dramatic diversification of functional properties can arise via minimal structural alterations. We suggest a novel structure-based mechanism of the steroid isomerization reaction.


    Organizational Affiliation

    Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, Latvia, Sweden. kaspars@biomed.lu.lv



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTATHIONE S-TRANSFERASE A3
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
222Homo sapiensMutation(s): 0 
Gene Names: GSTA3
EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q16772 (Homo sapiens)
Explore Q16772 
Go to UniProtKB:  Q16772
PHAROS:  Q16772
GTEx:  ENSG00000174156 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16772
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download Ideal Coordinates CCD File 
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
IA [auth K],
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
IA [auth K],
KA [auth L],
MA [auth M],
NA [auth N],
OA [auth O],
PA [auth P],
Q [auth A],
S [auth B],
U [auth C],
V [auth D],
X [auth E],
Z [auth F]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
ASD
Query on ASD

Download Ideal Coordinates CCD File 
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
JA [auth K],
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
JA [auth K],
LA [auth L],
QA [auth P],
R [auth A],
T [auth B],
W [auth D],
Y [auth E]
4-ANDROSTENE-3-17-DIONE
C19 H26 O2
AEMFNILZOJDQLW-QAGGRKNESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.177α = 89.76
b = 92.064β = 89.72
c = 113.54γ = 89.73
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.2: 2019-05-29
    Changes: Data collection, Experimental preparation, Other