6OMS

Arabidopsis GH3.12 with Chorismate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.942 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 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. --: --

  • DOI: 10.1074/jbc.RA119.009949

  • 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 9 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, a precursor of aromatic amino acids and salicylic acid, to cysteine and glutamate, 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 altered growth and no increased susceptibility to the pathogen Pseudomonas syringae, unlike gh3.12 mutants, which ere more susceptible than wild-type 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

    Biology, Washington University in St. Louis, United States.,Washington University in St. Louis, United States.,CNRS, France.,University of Nebraska.




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: GH3.12 (GDG1, PBS3, WIN3)
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
ISJ
Query on ISJ

Download SDF File 
Download CCD File 
B
(3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylic acid
Chorismic Acid
C10 H10 O6
WTFXTQVDAKGDEY-HTQZYQBOSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.942 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.438α = 90.00
b = 67.002β = 106.36
c = 100.964γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references