6D3M

FT_T dioxygenase with bound quizalofop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops.

Larue, C.T.Goley, M.Shi, L.Evdokimov, A.G.Sparks, O.C.Ellis, C.Wollacott, A.M.Rydel, T.J.Halls, C.E.Van Scoyoc, B.Fu, X.Nageotte, J.R.Adio, A.M.Zheng, M.Sturman, E.J.Garvey, G.S.Varagona, M.J.

(2019) Pest Manag Sci 75: 2086-2094

  • DOI: https://doi.org/10.1002/ps.5393
  • Primary Citation of Related Structures:  
    6D0O, 6D1O, 6D3H, 6D3I, 6D3J, 6D3M

  • PubMed Abstract: 

    Effective management of weedy species in agricultural fields is essential for maintaining favorable growing conditions and crop yields. The introduction of genetically modified crops containing herbicide tolerance traits has been a successful additional tool available to farmers to better control weeds. However, weed resistance challenges present a need for additional herbicide tolerance trait options. To help meet this challenge, a new trait that provides tolerance to an aryloxyphenoxypropionate (FOP) herbicide and members of the synthetic auxin herbicide family, such as 2,4-dichlorophenoxyacetic acid (2,4-D), was developed. Development of this herbicide tolerance trait employed an enzyme engineered with robust and specific enzymatic activity for these two herbicide families. This engineering effort utilized a microbial-sourced dioxygenase scaffold to generate variants with improved enzymatic parameters. Additional optimization to enhance in-plant stability of the enzyme enabled an efficacious trait that can withstand the higher temperature conditions often found in field environments. Optimized herbicide tolerance enzyme variants with enhanced enzymatic and temperature stability parameters enabled robust herbicide tolerance for two herbicide families in transgenic maize and soybeans. This herbicide tolerance trait for FOP and synthetic auxin herbicides such as 2,4-D could be useful in weed management systems, providing additional tools for farmers to control weeds. © 2019 Society of Chemical Industry.


  • Organizational Affiliation

    Bayer Crop Science, Plant Biotechnology, Chesterfield, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FT_T dioxygenaseA,
B,
C [auth F],
D [auth J]
295Sphingobium herbicidovoransMutation(s): 0 
Gene Names: rdpA
EC: 1.14.11.44
UniProt
Find proteins for Q8KSC8 (Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / CCUG 56400 / KCTC 2939 / LMG 18315 / NBRC 16415 / MH))
Explore Q8KSC8 
Go to UniProtKB:  Q8KSC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KSC8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FTJ
Query on FTJ

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth F],
Q [auth J]
(2R)-2-{4-[(6-chloroquinoxalin-2-yl)oxy]phenoxy}propanoic acid
C17 H13 Cl N2 O4
ABOOPXYCKNFDNJ-SNVBAGLBSA-N
AKG
Query on AKG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth F],
R [auth J]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth F],
P [auth J]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
O [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.778α = 90
b = 137.778β = 90
c = 148.346γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description