1GSH

STRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.208 

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:  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 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: 
    • 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: 1548
    • 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
    • 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
    • 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
    • Flexibility Impaired by Mutations Revealed the Multifunctional 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 A Resolution
      Yamaguchi, H.,Kato, H.,Hata, Y.,Nishioka, T.,Kimura, A.,Oda, J.,Katsube, Y.
      (1993) J.Mol.Biol. 229: 1083


    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)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 Å
  • R-Value Work: 0.208 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 87.800α = 90.00
b = 87.800β = 90.00
c = 170.000γ = 120.00
Software Package:
Software NamePurpose
WEISdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-07-11
    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: 2014-02-19
    Type: Database references