1GSA

STRUCTURE OF GLUTATHIONE SYNTHETASE COMPLEXED WITH ADP AND GLUTATHIONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1GSA

  • 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 structure represents a pseudo enzyme-substrate complex in the reverse reaction and consequently allows us to understand the active site architecture of the E ...

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

    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTATHIONE SYNTHETASEA316Escherichia coli BMutation(s): 0 
EC: 6.3.2.3
UniProt
Find proteins for P04425 (Escherichia coli (strain K12))
Explore P04425 
Go to UniProtKB:  P04425
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GSH (Subject of Investigation/LOI)
Query on GSH

Download Ideal Coordinates CCD File 
F [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.25α = 90
b = 87.25β = 90
c = 169.58γ = 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: 1996-06-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance