2GLT

STRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 6.0.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 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

  • Primary Citation of Related Structures:  

  • 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 t ...

    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: 
    • 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
    • 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
    • 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
    • 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
    • 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
    • Overexpression of Glutathione Synthase in Escherichia Coli
      Kato, H.,Kobayashi, M.,Murata, K.,Nishioka, T.,Oda, J.
      (1989) Agric.Biol.Chem. 53: 3071
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE BIOSYNTHETIC LIGASE
A
316Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gshB (gsh-II)
EC: 6.3.2.3
Find proteins for P04425 (Escherichia coli (strain K12))
Go to UniProtKB:  P04425
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.202 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 88.000α = 90.00
b = 88.000β = 90.00
c = 164.200γ = 120.00
Software Package:
Software NamePurpose
WEISdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2014-03-12
    Type: Other