1M0W | pdb_00001m0w

Yeast Glutathione Synthase Bound to gamma-glutamyl-cysteine, AMP-PNP and 2 Magnesium Ions

• PDB DOI: https://doi.org/10.2210/pdb1M0W/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-06-14 Released: 2002-12-11 
• Deposition Author(s): Gogos, A., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.196 (Depositor) 
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Large Conformational Changes in the Catalytic Cycle of Glutathione Synthase

Gogos, A., Shapiro, L.

(2002) Structure 10: 1669-1676

• PubMed: 12467574 
• DOI: https://doi.org/10.1016/s0969-2126(02)00906-1
• Primary Citation Related Structures: 
  1M0T, 1M0W


• PubMed Abstract: 
  

  Glutathione synthase catalyzes the final ATP-dependent step in glutathione biosynthesis, the formation of glutathione from gamma-glutamylcysteine and glycine. We have determined structures of yeast glutathione synthase in two forms: unbound (2.3 A resolution) and bound to its substrate gamma-glutamylcysteine, the ATP analog AMP-PNP, and two magnesium ions (1.8 A resolution). These structures reveal that upon substrate binding, large domain motions convert the enzyme from an open unliganded form to a closed conformation in which protein domains completely surround the substrate in the active site.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 114.04 kDa 
• Atom Count: 8,810 
• Modeled Residue Count: 960 
• Deposited Residue Count: 982 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glutathione synthetase	A, B	491	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: GSH2 EC: 6.3.2.3
UniProt
Find proteins for Q08220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08220  Go to UniProtKB:  Q08220

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	H [auth A], P [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
3GC	I [auth A], Q [auth B]	GAMMA-GLUTAMYLCYSTEINE C8 H14 N2 O5 S RITKHVBHSGLULN-WHFBIAKZSA-N
SO4	E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], D [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.196 (Depositor) 
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.661	α = 82.08
b = 52.006	β = 86.77
c = 100.636	γ = 77.49

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-11 
Deposition Author(s): Gogos, A., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2002-12-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Refinement description