Crystal structure of GAD1 from Arabidopsis thaliana

Experimental Data Snapshot

  • Resolution: 2.67 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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This is version 1.4 of the entry. See complete history


A common structural basis for pH- and calmodulin-mediated regulation in plant glutamate decarboxylase.

Gut, H.Dominici, P.Pilati, S.Astegno, A.Petoukhov, M.V.Svergun, D.I.Grutter, M.G.Capitani, G.

(2009) J Mol Biol 392: 334-351

  • DOI: https://doi.org/10.1016/j.jmb.2009.06.080
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Glutamate decarboxylase (Gad) catalyzes glutamate to gamma-aminobutyrate conversion. Plant Gad is a approximately 340 kDa hexamer, involved in development and stress response, and regulated by pH and binding of Ca(2+)/calmodulin (CaM) to the C-terminal domain. We determined the crystal structure of Arabidopsis thaliana Gad1 in its CaM-free state, obtained a low-resolution structure of the calmodulin-activated Gad complex by small-angle X-ray scattering and identified the crucial residues, in the C-terminal domain, for regulation by pH and CaM binding. CaM activates Gad1 in a unique way by relieving two C-terminal autoinhibition domains of adjacent active sites, forming a 393 kDa Gad1-CaM complex with an unusual 1:3 stoichiometry. The complex is loosely packed: thanks to the flexible linkers connecting the enzyme core with the six C-terminal regulatory domains, the CaM molecules retain considerable positional and orientational freedom with respect to Gad1. The complex thus represents a prototype for a novel CaM-target interaction mode. Thanks to its two levels of regulation, both targeting the C-terminal domain, Gad can respond flexibly to different kinds of cellular stress occurring at different pH values.

  • Organizational Affiliation

    Biochemisches Institut, Universität Zürich, Zürich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate decarboxylase 1
A, B, C, D, E
A, B, C, D, E, F
502Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g17330GADGAD1GDH1MKP11.30MKP11_18
Find proteins for Q42521 (Arabidopsis thaliana)
Explore Q42521 
Go to UniProtKB:  Q42521
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42521
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on LLP
A, B, C, D, E
A, B, C, D, E, F
Experimental Data & Validation

Experimental Data

  • Resolution: 2.67 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.098α = 90
b = 118.098β = 90
c = 200.576γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-22
    Changes: Data collection