3HBX

Crystal structure of GAD1 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.672 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2009.06.080

  • 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-termin ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate decarboxylase 1
A, B, C, D, E, F
502Arabidopsis thalianaMutation(s): 0 
Gene Names: GAD1 (GAD, GDH1)
EC: 4.1.1.15
Find proteins for Q42521 (Arabidopsis thaliana)
Go to Gene View: GAD1
Go to UniProtKB:  Q42521
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D, E, F
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.672 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.208 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 118.098α = 90.00
b = 118.098β = 90.00
c = 200.576γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description