9FWD | pdb_00009fwd

Structure of indole-3-acetic acid-amido synthetase GH3.6 from A.thaliana in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.240 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Phenylacetic acid metabolism in land plants: novel pathways and metabolites.

Hladik, P.Brunoni, F.Zukauskaite, A.Zatloukal, M.Belicek, J.Kopecny, D.Briozzo, P.Ferchaud, N.Novak, O.Pencik, A.

(2025) J Exp Bot 76: 3427-3443

  • DOI: https://doi.org/10.1093/jxb/eraf092
  • Primary Citation of Related Structures:  
    9FWD, 9FXD

  • PubMed Abstract: 

    In recent years, substantial progress has been made in exploring auxin conjugation and metabolism, primarily aiming at indole-3-acetic acid (IAA). However, the metabolic regulation of another key auxin, phenylacetic acid (PAA), remains largely uncharacterized. Here, we provide a comprehensive exploration of PAA metabolism in land plants. Through LC-MS screening across multiple plant species and their organs, we identified four previously unreported endogenous PAA metabolites: phenylacetyl-leucine (PAA-Leu), phenylacetyl-phenylalanine (PAA-Phe), phenylacetyl-valine (PAA-Val), and phenylacetyl-glucose (PAA-glc). Enzyme assays, genetic evidence, crystal structures, and docking studies demonstrate that PAA and IAA share core metabolic machinery, revealing a complex regulatory network that maintains auxin homeostasis. Furthermore, our study of PAA conjugation with amino acids and glucose suggests limited compensatory mechanisms within known conjugation pathways, pointing to the existence of alternative metabolic routes in land plants. These insights advance our knowledge of auxin-specific metabolic networks and highlight the unique complexity within plant hormone regulation.


  • Organizational Affiliation
    • Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences & Faculty of Science, Palacký University, Olomouc, Czech Republic.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indole-3-acetic acid-amido synthetase GH3.6
A, B
620Arabidopsis thalianaMutation(s): 0 
Gene Names: GH3.6DFL1At5g54510F24B18.13
EC: 6.3.2
UniProt
Find proteins for Q9LSQ4 (Arabidopsis thaliana)
Explore Q9LSQ4 
Go to UniProtKB:  Q9LSQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LSQ4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.240 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.975α = 90
b = 196.975β = 90
c = 65.206γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
autoPROCdata processing
Aimlessdata scaling
BUSTERrefinement
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Palacky University in OlomoucCzech RepublicIGA_PrF_2023_012
Agence Nationale de la Recherche (ANR)FranceANR-11-IDEX-0003

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Database references