1GSA

STRUCTURE OF GLUTATHIONE SYNTHETASE COMPLEXED WITH ADP AND GLUTATHIONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution.

Hara, T.Kato, H.Katsube, Y.Oda, J.

(1996) Biochemistry 35: 11967-11974

  • DOI: 10.1021/bi9605245

  • PubMed Abstract: 
  • The crystal structure of glutathione synthetase from Escherichia coli B complexed with ADP, glutathione, and sulfate has been determined at 2.0 A resolution. Concerning the chemical similarity of sulfate and phosphate, this quaternary complex structu ...

    The crystal structure of glutathione synthetase from Escherichia coli B complexed with ADP, glutathione, and sulfate has been determined at 2.0 A resolution. Concerning the chemical similarity of sulfate and phosphate, this quaternary complex structure represents a pseudo enzyme-substrate complex in the reverse reaction and consequently allows us to understand the active site architecture of the E. coli glutathione synthetase. Two Mg2+ ions are coordinated with oxygen atoms from the alpha- and beta-phosphate groups of ADP and from the sulfate ion. The flexible loops, invisible in the unliganded or the binary and ternary complex structures, are fixed in the quaternary complex. The larger flexible loop (Ile226-Arg241) includes one turn of a 310-helix that comprises the binding site of the glycine moiety of GSH. The small loop (Gly164-Gly167) is involved in nucleotide binding and acts as a phosphate gripper. The side chains of Arg210 and Arg225 interact with the sulfate ion and the beta-phosphate moiety of ADP. Arg 210 is likely to interact with the carboxylate of the C-terminal gamma-glutamylcysteine in the substrate-binding form of the forward reaction. Other positively charged residues in the active site (Lys125 and Lys160) are involved in nucleotide binding, directing the phosphate groups to the right position for catalysis. Functional aspects of the active site architecture in the substrate-binding form are discussed.


    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
    • 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
    • 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
    • Role of Cysteine Residues in Glutathione Synthetase from Escherichia Coli B. Chemical Modification and Oligonucleotide Site-Directed Mutagenesis
      Kato, H.,Tanaka, T.,Nishioka, T.,Kimura, A.,Oda, J.
      (1988) J.Biol.Chem. 263: 11646
    • Overexpression of Glutathione Synthetase in Escherichia Coli
      Kato, H.,Kobayashi, M.,Murata, K.,Nishioka, T.,Oda, J.
      (1989) Agric.Biol.Chem. 53: 3071


    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE SYNTHETASE
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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GSH
Query on GSH

Download SDF File 
Download CCD File 
A
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.188 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 87.250α = 90.00
b = 87.250β = 90.00
c = 169.580γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
WEISdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-06-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance