Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

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Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins.

Matsuda, K.Mizuguchi, K.Nishioka, T.Kato, H.Go, N.Oda, J.

(1996) Protein Eng 9: 1083-1092

  • DOI: https://doi.org/10.1093/protein/9.12.1083
  • Primary Citation of Related Structures:  
    1GSH, 2GLT

  • PubMed Abstract: 

    The crystal structure of Escherichia coli B glutathione synthetase (GSHase) has been determined at the optimal catalytic condition pH 7.5. The most significant structural difference from the structure at pH 6.0 is the movement of the central domain towards the N-terminal domain almost as a rigid body. As a result of this movement, new interdomain and intersubunit polar interactions are formed which stabilize the dimeric structure further. The structure of GSHase at optimal pH was compared with 294 other known protein structures in terms of the spatial arrangements of secondary structural elements. Three enzymes (D-alanine: D-alanine ligase, succinyl-CoA synthetase and the biotin carboxylase subunit of acetyl-CoA carboxylase) were found to have structures similar to the ATP-binding site of GSHase, which extends across two domains. The ATP-binding sites in these four enzymes are composed of two antiparallel beta-sheets and are different from the classic mononucleotide-binding fold. Except for these proteins, no significant structural similarity was detected between GSHase and the other ATP-binding proteins. A structural motif in the N-terminal domain of GSHase has been found to be similar to the NAD-binding fold. This structural motif is shared by a number of other proteins that bind various negatively charged molecules.

  • Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTATHIONE BIOSYNTHETIC LIGASE316Escherichia coli BMutation(s): 0 
Gene Names: GSHII
Find proteins for P04425 (Escherichia coli (strain K12))
Explore P04425 
Go to UniProtKB:  P04425
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04425
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88α = 90
b = 88β = 90
c = 164.2γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
WEISdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2014-03-12
    Changes: Other
  • Version 1.4: 2023-05-31
    Changes: Data collection, Database references, Other
  • Version 1.5: 2024-05-29
    Changes: Data collection