3KAK

Structure of homoglutathione synthetase from Glycine max in open conformation with gamma-glutamyl-cysteine bound.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

Starting Model: other
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This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Evolution of Product Diversity in Soybean Glutathione Biosynthesis.

Galant, A.Arkus, K.A.Zubieta, C.Cahoon, R.E.Jez, J.M.

(2009) Plant Cell 21: 3450-3458

  • DOI: https://doi.org/10.1105/tpc.109.071183
  • Primary Citation of Related Structures:  
    3KAJ, 3KAK, 3KAL

  • PubMed Abstract: 

    The redox active peptide glutathione is ubiquitous in nature, but some plants also synthesize glutathione analogs in response to environmental stresses. To understand the evolution of chemical diversity in the closely related enzymes homoglutathione synthetase (hGS) and glutathione synthetase (GS), we determined the structures of soybean (Glycine max) hGS in three states: apoenzyme, bound to gamma-glutamylcysteine (gammaEC), and with hGSH, ADP, and a sulfate ion bound in the active site. Domain movements and rearrangement of active site loops change the structure from an open active site form (apoenzyme and gammaEC complex) to a closed active site form (hGSH*ADP*SO(4)(2-) complex). The structure of hGS shows that two amino acid differences in an active site loop provide extra space to accommodate the longer beta-Ala moiety of hGSH in comparison to the glycinyl group of glutathione. Mutation of either Leu-487 or Pro-488 to an Ala improves catalytic efficiency using Gly, but a double mutation (L487A/P488A) is required to convert the substrate preference of hGS from beta-Ala to Gly. These structures, combined with site-directed mutagenesis, reveal the molecular changes that define the substrate preference of hGS, explain the product diversity within evolutionarily related GS-like enzymes, and reinforce the critical role of active site loops in the adaptation and diversification of enzyme function.


  • Organizational Affiliation

    Department of Biology, Washington University, St. Louis, Missouri 63130, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homoglutathione synthetase
A, B
499Glycine maxMutation(s): 0 
Gene Names: hGS
EC: 6.3.2.3
UniProt
Find proteins for Q9M426 (Glycine max)
Explore Q9M426 
Go to UniProtKB:  Q9M426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M426
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.88α = 90
b = 80.95β = 95.96
c = 89.12γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    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
  • Version 1.3: 2024-04-03
    Changes: Refinement description