4L39

Crystal structure of GH3.12 from Arabidopsis thaliana in complex with AMPCPP and salicylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography.

Round, A.Brown, E.Marcellin, R.Kapp, U.Westfall, C.S.Jez, J.M.Zubieta, C.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2072-2080

  • DOI: https://doi.org/10.1107/S0907444913019276
  • Primary Citation of Related Structures:  
    4L39

  • PubMed Abstract: 

    The combination of protein crystallography and small-angle X-ray scattering (SAXS) provides a powerful method to investigate changes in protein conformation. These complementary structural techniques were used to probe the solution structure of the apo and the ligand-bound forms of the Arabidopsis thaliana acyl acid-amido synthetase GH3.12. This enzyme is part of the extensive GH3 family and plays a critical role in the regulation of plant hormones through the formation of amino-acid-conjugated hormone products via an ATP-dependent reaction mechanism. The enzyme adopts two distinct C-terminal domain orientations with `open' and `closed' active sites. Previous studies suggested that ATP only binds in the open orientation. Here, the X-ray crystal structure of GH3.12 is presented in the closed conformation in complex with the nonhydrolysable ATP analogue AMPCPP and the substrate salicylate. Using on-line HPLC purification combined with SAXS measurements, the most likely apo and ATP-bound protein conformations in solution were determined. These studies demonstrate that the C-terminal domain is flexible in the apo form and favours the closed conformation upon ATP binding. In addition, these data illustrate the efficacy of on-line HPLC purification integrated into the SAXS sample-handling environment to reliably monitor small changes in protein conformation through the collection of aggregate-free and highly redundant data.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-substituted benzoates-glutamate ligase GH3.12
A, B
581Arabidopsis thalianaMutation(s): 0 
Gene Names: GH3.12GDG1PBS3WIN3At5g13320T22N19.5T31B5.140
EC: 6.3.2
UniProt
Find proteins for Q9LYU4 (Arabidopsis thaliana)
Explore Q9LYU4 
Go to UniProtKB:  Q9LYU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LYU4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.36α = 90
b = 114.088β = 90
c = 157.976γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Experimental preparation
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description