3GKE

Crystal Structure of Dicamba Monooxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation.

Dumitru, R.Jiang, W.Z.Weeks, D.P.Wilson, M.A.

(2009) J Mol Biol 392: 498-510

  • DOI: https://doi.org/10.1016/j.jmb.2009.07.021
  • Primary Citation of Related Structures:  
    3GKE, 3GL0, 3GL2

  • PubMed Abstract: 

    Dicamba (3,6-dichloro-2-methoxybenzoic acid) is a widely used herbicide that is efficiently degraded by soil microbes. These microbes use a novel Rieske nonheme oxygenase, dicamba monooxygenase (DMO), to catalyze the oxidative demethylation of dicamba to 3,6-dichlorosalicylic acid (DCSA) and formaldehyde. We have determined the crystal structures of DMO in the free state, bound to its substrate dicamba, and bound to the product DCSA at 2.10-1.75 A resolution. The structures show that the DMO active site uses a combination of extensive hydrogen bonding and steric interactions to correctly orient chlorinated, ortho-substituted benzoic-acid-like substrates for catalysis. Unlike other Rieske aromatic oxygenases, DMO oxygenates the exocyclic methyl group, rather than the aromatic ring, of its substrate. This first crystal structure of a Rieske demethylase shows that the Rieske oxygenase structural scaffold can be co-opted to perform varied types of reactions on xenobiotic substrates.


  • Organizational Affiliation

    Department of Biochemistry, The University of Nebraska-Lincoln, Lincoln, NE 68588-0664, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DdmC
A, B, C
349Stenotrophomonas maltophiliaMutation(s): 0 
Gene Names: ddmC
EC: 1.14.15
UniProt
Find proteins for Q5S3I3 (Stenotrophomonas maltophilia)
Explore Q5S3I3 
Go to UniProtKB:  Q5S3I3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5S3I3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
R [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
O [auth B]
P [auth B]
F [auth A],
G [auth A],
H [auth A],
O [auth B],
P [auth B],
Q [auth B],
S [auth C],
T [auth C],
U [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
N [auth B],
V [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
M [auth B]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.026α = 90
b = 81.026β = 90
c = 158.154γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SHELXDEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description