2GRT | pdb_00002grt

HUMAN GLUTATHIONE REDUCTASE A34E, R37W MUTANT, OXIDIZED GLUTATHIONE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 
    0.189 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

Glutathione reductase turned into trypanothione reductase: structural analysis of an engineered change in substrate specificity.

Stoll, V.S.Simpson, S.J.Krauth-Siegel, R.L.Walsh, C.T.Pai, E.F.

(1997) Biochemistry 36: 6437-6447

  • DOI: https://doi.org/10.1021/bi963074p
  • Primary Citation Related Structures: 
    1GRT, 2GRT, 3GRT, 4GRT, 5GRT

  • PubMed Abstract: 

    Trypanosoma and Leishmania, pathogens responsible for diseases such as African sleeping sickness, Chagas' heart disease, or Oriental sore, are two of the very few genera that do not use the ubiquitous glutathione/glutathione reductase system to keep a stable cellular redox balance. Instead, they rely on trypanothione and trypanothione reductase to protect them from oxidative stress. Trypanothione reductase (TR) and the corresponding host enzyme, human red blood cell glutathione reductase (GR), belong to the same flavoprotein family. Despite their closely related three-dimensional structures and although their natural substrates share the common structural glutathione core, the two enzymes are mutually exclusive with respect to their disulfide substrates. This makes the parasite enzyme a potential target for antitrypanosomal drug design. While a large body of structural data on GR complexes is available, information on TR-ligand interactions is very limited. When the two amino acid changes Ala34Glu and Arg37Trp are introduced into human GR, the resulting mutant enzyme (GRTR) prefers trypanothione 700-fold over its original substrate, effectively converting a GR into a TR [Bradley, M., Bücheler, U. S., & Walsh, C. T. (1991) Biochemistry 30, 6124-6127]. The crystal structure of GRTR has been determined at 2.3 A resolution and refined to a crystallographic R factor of 20.9%. We have taken advantage of the ease with which ligand complexes can be produced in GR crystals, a property that extends to the isomorphous GRTR crystals, and have produced and analyzed crystals of GRTR complexes with glutathione, trypanothione, glutathionylspermidine and of a true catalytic intermediate, the mixed disulfide between trypanothione and the enzyme. The corresponding molecular structures have been characterized at resolutions between 2.3 and 2.8 A with R factors ranging from 17.1 to 19.7%. The results indicate that the Ala34Glu mutation causes steric hindrance leading to a large displacement of the side chain of Arg347. This movement combined with the change in charge introduced by the mutations modifies the binding cavity, forcing glutathione to adopt a nonproductive binding mode and permitting trypanothione and to a certain degree also the weak substrate glutathionylspermidine to assume a productive mode.


  • Organizational Affiliation
    • Department of Biochemistry, University of Toronto, Ontario Cancer Institute, Canada.

Macromolecule Content 

  • Total Structure Weight: 51.46 kDa 
  • Atom Count: 3,599 
  • Modeled Residue Count: 461 
  • Deposited Residue Count: 461 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUTATHIONE REDUCTASE461Homo sapiensMutation(s): 2 
EC: 1.6.4.2 (PDB Primary Data), 1.8.1.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00390 (Homo sapiens)
Explore P00390 
Go to UniProtKB:  P00390
PHAROS:  P00390
GTEx:  ENSG00000104687 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00390
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GDS

Query on GDS



Download:Ideal Coordinates CCD File
C [auth A]OXIDIZED GLUTATHIONE DISULFIDE
C20 H32 N6 O12 S2
YPZRWBKMTBYPTK-BJDJZHNGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work:  0.189 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: B 1 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.4α = 90
b = 84.53β = 90
c = 63.46γ = 58.71
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-08-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-09
    Changes: Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection
  • Version 1.6: 2024-10-30
    Changes: Structure summary