2GLT

STRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 6.0.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 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 ...

    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.


    Related Citations: 
    • Flexible Loop that is Novel Catalytic Machinery in a Ligase. Atomic Structure and Function of the Loopless Glutathione Synthetase
      Kato, H., Tanaka, T., Yamaguchi, H., Hara, T., Nishioka, T., Katsube, Y., Oda, J.
      (1994) Biochemistry 33: 4995
    • Mechanism-Based Inactivation of Glutathione Synthetase by Phosphinic Acid Transition-State Analogue
      Hiratake, J., Kato, H., Oda, J.
      (1994) J Am Chem Soc 116: 12059
    • Use of Adenosine (5')Polyphospho(5')Pyridoxals to Study the Substrate-Binding Region of Glutathione Synthetase from Escherichia Coli B
      Hibi, T., Kato, H., Nishioka, T., Oda, J., Yamaguchi, H., Katsube, Y., Tanizawa, K., Fukui, T.
      (1993) Biochemistry 32: 1545
    • Flexibility Impaired by Mutations Revealed the Multi-Functional Roles of the Loop in Glutathione Synthetase
      Tanaka, T., Yamaguchi, H., Kato, H., Nishioka, T., Katsube, Y., Oda, J.
      (1993) Biochemistry 32: 12398
    • Three-Dimensional Structure of the Glutathione Synthetase from Escherichia Coli B at 2.0 Angstroms Resolution
      Yamaguchi, H., Kato, H., Hata, Y., Nishioka, T., Kimura, A., Oda, J., Katsube, Y.
      (1993) J Mol Biol 229: 1083
    • Construction, Expression, and Characterization of Glutathione Synthetase Chimeras: Substitution of a Homologous Loop Peptide Region of Dihydrofolate Reductase
      Tanaka, T., Sakai, T., Chihara-Siomi, M., Takeshima, K., Kato, H., Misawa, T., Nishioka, T., Oda, J.
      (1993) Bull Inst Chem Res ,kyoto Univ 71: 274
    • Mutational and Proteolytic Studies on a Flexible Loop in Glutathione Synthetase from Escherichia Coli B: The Loop and Arginine 233 are Critical for the Catalytic Reaction
      Tanaka, T., Kato, H., Nishioka, T., Oda, J.
      (1992) Biochemistry 31: 2259
    • Structural Studies on Glutathione Synthetase from Escherichia Coli B
      Yamaguchi, H., Kato, H., Hata, Y., Nishioka, T., Oda, J., Katsube, Y.
      (1992) Photon Factory Activity Report 9: 85
    • Crystallization and Preliminary X-Ray Studies of Glutathione Synthetase from Escherichia Coli B
      Kato, H., Yamaguchi, H., Hata, Y., Nishioka, T., Katsube, Y., Oda, J.
      (1989) J Mol Biol 209: 503
    • Overexpression of Glutathione Synthase in Escherichia Coli
      Kato, H., Kobayashi, M., Murata, K., Nishioka, T., Oda, J.
      (1989) Agric Biol Chem 53: 3071
    • Role of Cysteine Residues in Glutathione Synthetase from Escherchia Coli B
      Kato, H., Tanaka, T., Nishioka, T., Kimura, A., Oda, J.
      (1988) J Biol Chem 263: 11646
    • Complete Nucleotide Sequence of E.Coli Glutathione Synthetase Gsh-II
      Gushima, H., Yasuda, S., Soeda, E., Yokota, M., Kondo, M., Kimura, A.
      (1984) Nucleic Acids Res 12: 9299

    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTATHIONE BIOSYNTHETIC LIGASEA316Escherichia coli BMutation(s): 0 
Gene Names: GSHII
EC: 6.3.2.3
UniProt
Find proteins for P04425 (Escherichia coli (strain K12))
Explore P04425 
Go to UniProtKB:  P04425
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
X-PLORrefinement
WEISdata reduction
X-PLORphasing

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