3GL0

Crystal structure of dicamba monooxygenase bound to 3,6 dichlorosalicylic acid (DCSA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DdmCA, B, C349Stenotrophomonas maltophiliaMutation(s): 0 
Gene Names: ddmC
EC: 1.14.15
UniProt
Find proteins for Q5S3I3 (Stenotrophomonas maltophilia)
Explore Q5S3I3 
Go to UniProtKB:  Q5S3I3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HXX (Subject of Investigation/LOI)
Query on HXX

Download Ideal Coordinates CCD File 
F [auth A], N [auth B]3,6-dichloro-2-hydroxybenzoic acid
C7 H4 Cl2 O3
FKIKPQHMWFZFEB-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , O [auth B] , P [auth B] , Q [auth B] , R [auth B] , T [auth C] , 
H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], V [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.205α = 90
b = 81.205β = 90
c = 158.557γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SHELXDEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance