6OMS

Arabidopsis GH3.12 with Chorismate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Brassicaceae-specific Gretchen Hagen 3 acyl acid amido synthetases conjugate amino acids to chorismate, a precursor of aromatic amino acids and salicylic acid.

Holland, C.K.Westfall, C.S.Schaffer, J.E.De Santiago, A.Zubieta, C.Alvarez, S.Jez, J.M.

(2019) J Biol Chem 294: 16855-16864

  • DOI: 10.1074/jbc.RA119.009949
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • To modulate responses to developmental or environmental cues, plants use Gretchen Hagen 3 (GH3) acyl acid amido synthetases to conjugate an amino acid to a plant hormone, a reaction that regulates free hormone concentration and downstream responses. ...

    To modulate responses to developmental or environmental cues, plants use Gretchen Hagen 3 (GH3) acyl acid amido synthetases to conjugate an amino acid to a plant hormone, a reaction that regulates free hormone concentration and downstream responses. The model plant Arabidopsis thaliana has 19 GH3 proteins, of which 8 have confirmed biochemical functions. One Brassicaceae-specific clade of GH3 proteins was predicted to use benzoate as a substrate and includes AtGH3.7 and AtGH3.12/PBS3. Previously identified as a 4-hydroxybenzoic acid-glutamate synthetase, AtGH3.12/PBS3 influences pathogen defense responses through salicylic acid. Recent work has shown that AtGH3.12/PBS3 uses isochorismate as a substrate, forming an isochorismate-glutamate conjugate that converts into salicylic acid. Here, we show that AtGH3.7 and AtGH3.12/PBS3 can also conjugate chorismate to cysteine and glutamate, which act as precursors to aromatic amino acids and salicylic acid, respectively. The X-ray crystal structure of AtGH3.12/PBS3 in complex with AMP and chorismate at 1.94 Å resolution, along with site-directed mutagenesis, revealed how the active site potentially accommodates this substrate. Examination of Arabidopsis knockout lines indicated that the gh3.7 mutants do not alter growth and showed no increased susceptibility to the pathogen Pseudomonas syringae , unlike gh3.12 mutants, which were more susceptible than WT plants, as was the gh3.7 / gh3.12 double mutant. The findings of our study suggest that GH3 proteins can use metabolic precursors of aromatic amino acids as substrates.


    Organizational Affiliation

    Department of Biology, Washington University, St. Louis, Missouri 63130 jjez@wustl.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-substituted benzoates-glutamate ligase GH3.12
A, B
575Arabidopsis thalianaMutation(s): 0 
Gene Names: GH3.12GDG1PBS3WIN3At5g13320T22N19.5T31B5.140
EC: 6.3.2
Find proteins for Q9LYU4 (Arabidopsis thaliana)
Go to UniProtKB:  Q9LYU4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
ISJ
Query on ISJ

Download CCD File 
B
(3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid
C10 H10 O6
WTFXTQVDAKGDEY-HTQZYQBOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.438α = 90
b = 67.002β = 106.36
c = 100.964γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1614539

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence