4EQL

Crystal Structure of GH3.12 in complex with AMP and salicylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for prereceptor modulation of plant hormones by GH3 proteins.

Westfall, C.S.Zubieta, C.Herrmann, J.Kapp, U.Nanao, M.H.Jez, J.M.

(2012) Science 336: 1708-1711

  • DOI: https://doi.org/10.1126/science.1221863
  • Primary Citation of Related Structures:  
    4EPL, 4EPM, 4EQ4, 4EQL, 4EWV

  • PubMed Abstract: 

    Acyl acid amido synthetases of the GH3 family act as critical prereceptor modulators of plant hormone action; however, the molecular basis for their hormone selectivity is unclear. Here, we report the crystal structures of benzoate-specific Arabidopsis thaliana AtGH3.12/PBS3 and jasmonic acid-specific AtGH3.11/JAR1. These structures, combined with biochemical analysis, define features for the conjugation of amino acids to diverse acyl acid substrates and highlight the importance of conformational changes in the carboxyl-terminal domain for catalysis. We also identify residues forming the acyl acid binding site across the GH3 family and residues critical for amino acid recognition. Our results demonstrate how a highly adaptable three-dimensional scaffold is used for the evolution of promiscuous activity across an enzyme family for modulation of plant signaling molecules.


  • Organizational Affiliation

    Department of Biology, Washington University, St. Louis, MO 63130, USA.


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: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.42α = 90
b = 66.58β = 106.48
c = 101γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description