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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.,Sect.D 69: 2072-2080

  • DOI: 10.1107/S0907444913019276

  • 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 a ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-substituted benzoates-glutamate ligase GH3.12
A, B
581Arabidopsis thalianaMutation(s): 0 
Gene Names: GH3.12 (GDG1, PBS3, WIN3)
EC: 6.3.2.-
Find proteins for Q9LYU4 (Arabidopsis thaliana)
Go to UniProtKB:  Q9LYU4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download SDF File 
Download CCD File 
A, B
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SAL
Query on SAL

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Download CCD File 
A, B
2-HYDROXYBENZOIC ACID
SALICYLIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.360α = 90.00
b = 114.088β = 90.00
c = 157.976γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
EDNAdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references
  • Version 1.2: 2018-02-07
    Type: Experimental preparation