3KAL

Structure of homoglutathione synthetase from Glycine max in closed conformation with homoglutathione, ADP, a sulfate ion, and three magnesium ions bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1105/tpc.109.071183
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
homoglutathione synthetase
A, B
499Glycine maxMutation(s): 0 
Gene Names: hGS
EC: 6.3.2.3
Find proteins for Q9M426 (Glycine max)
Go to UniProtKB:  Q9M426
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

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A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HGS
Query on HGS

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A, B
D-gamma-glutamyl-L-cysteinyl-beta-alanine
C11 H19 N3 O6 S
HKBNQXMLSMKLJV-RQJHMYQMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 115.700α = 90.00
b = 115.700β = 90.00
c = 101.760γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
HKL-2000data collection
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance