6LSV

Crystal structure of JOX2 in complex with 2OG, Fe, and JA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure-guided analysis of Arabidopsis JASMONATE-INDUCED OXYGENASE (JOX) 2 reveals key residues for recognition of jasmonic acid substrate by plant JOXs.

Zhang, X.Wang, D.Elberse, J.Qi, L.Shi, W.Peng, Y.L.Schuurink, R.C.Van den Ackerveken, G.Liu, J.

(2021) Mol Plant 14: 820-828

  • DOI: https://doi.org/10.1016/j.molp.2021.01.017
  • Primary Citation of Related Structures:  
    6LSV

  • PubMed Abstract: 

    The jasmonic acid (JA) signaling pathway is used by plants to control wound responses. The persistent accumulation of JA inhibits plant growth, and the hydroxylation of JA to 12-hydroxy-JA by JASMONATE-INDUCED OXYGENASEs (JOXs, also named jasmonic acid oxidases) is therefore vital for plant growth, while structural details of JA recognition by JOXs are unknown. Here, we present the 2.65 Å resolution X-ray crystal structure of Arabidopsis JOX2 in complex with its substrate JA and its co-substrates 2-oxoglutarate and Fe(II). JOX2 contains a distorted double-stranded β helix (DSBH) core flanked by α helices and loops. JA is bound in the narrow substrate pocket by hydrogen bonds with the arginine triad R225, R350, and R354 and by hydrophobic interactions mainly with the phenylalanine triad F157, F317, and F346. The most critical residues for JA binding are F157 and R225, both from the DSBH core, which interact with the cyclopentane ring of JA. The spatial distribution of critical residues for JA binding and the shape of the substrate-binding pocket together define the substrate selectivity of the JOXs. Sequence alignment shows that these critical residues are conserved among JOXs from higher plants. Collectively, our study provides insights into the mechanism by which higher plants hydroxylate the hormone JA.


  • Organizational Affiliation

    State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, Joint International Research Laboratory of Crop Molecular Breeding, College of Plant Protection, China Agricultural University, Beijing 100193, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable 2-oxoglutarate-dependent dioxygenase At5g05600
A, B
353Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g05600MOP10.14
EC: 1.14.11
UniProt
Find proteins for Q9FFF6 (Arabidopsis thaliana)
Explore Q9FFF6 
Go to UniProtKB:  Q9FFF6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FFF6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JAA (Subject of Investigation/LOI)
Query on JAA

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
{(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid
C12 H18 O3
ZNJFBWYDHIGLCU-HWKXXFMVSA-N
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.476α = 90
b = 74.416β = 110.04
c = 75.488γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFD0300700

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2021-03-17
    Changes: Database references
  • Version 1.3: 2021-05-12
    Changes: Database references
  • Version 1.4: 2023-11-29
    Changes: Data collection, Database references, Refinement description