6GMO | pdb_00006gmo

Plant glutamate cysteine ligase (GCL) in complex with non-reducing GSH (GSM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.198 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Plant glutathione biosynthesis revisited: redox-mediated activation of glutamylcysteine ligase does not require homo-dimerization.

Yang, Y.Lenherr, E.D.Gromes, R.Wang, S.Wirtz, M.Hell, R.Peskan-Berghofer, T.Scheffzek, K.Rausch, T.

(2019) Biochem J 476: 1191-1203

  • DOI: https://doi.org/10.1042/BCJ20190072
  • Primary Citation Related Structures: 
    6GMO

  • PubMed Abstract: 

    Plant γ-glutamylcysteine ligase (GCL), catalyzing the first and tightly regulated step of glutathione (GSH) biosynthesis, is redox-activated via formation of an intramolecular disulfide bond. In vitro , redox-activation of recombinant GCL protein causes formation of homo-dimers. Here, we have investigated whether dimerization occurs in vivo and if so whether it contributes to redox-activation. FPLC analysis indicated that recombinant redox-activated WT (wild type) AtGCL dissociates into monomers at concentrations below 10 -6  M, i.e. below the endogenous AtGCL concentration in plastids, which was estimated to be in the micromolar range. Thus, dimerization of redox-activated GCL is expected to occur in vivo To determine the possible impact of dimerization on redox-activation, AtGCL mutants were generated in which salt bridges or hydrophobic interactions at the dimer interface were interrupted. WT AtGCL and mutant proteins were analyzed by non-reducing SDS-PAGE to address their redox state and probed by FPLC for dimerization status. Furthermore, their substrate kinetics ( K M , V max ) were compared. The results indicate that dimer formation is not required for redox-mediated enzyme activation. Also, crystal structure analysis confirmed that dimer formation does not affect binding of GSH as competitive inhibitor. Whether dimerization affects other enzyme properties, e.g. GCL stability in vivo , remains to be investigated.


  • Organizational Affiliation
    • Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 102.41 kDa 
  • Atom Count: 8,447 
  • Modeled Residue Count: 877 
  • Deposited Residue Count: 892 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate--cysteine ligase, chloroplastic
A, B
446Brassica junceaMutation(s): 0 
Gene Names: GSH1ECS1
EC: 6.3.2.2
UniProt
Find proteins for O23736 (Brassica juncea)
Explore O23736 
Go to UniProtKB:  O23736
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO23736
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSM
(Subject of Investigation/LOI)

Query on GSM



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
L-GAMMA-GLUTAMYL-S-METHYLCYSTEINYLGLYCINE
C11 H19 N3 O6 S
QTQDDTSVRVWHMO-BQBZGAKWSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.198 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.77α = 90
b = 109.86β = 98.72
c = 84.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySPP1710

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary