3GL2 | pdb_00003gl2

Crystal structure of dicamba monooxygenase bound to dicamba


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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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 Biology 392: 498-510

  • DOI: https://doi.org/10.1016/j.jmb.2009.07.021
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 117.01 kDa 
  • Atom Count: 8,156 
  • Modeled Residue Count: 989 
  • Deposited Residue Count: 1,047 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D3M

Query on D3M



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
3,6-dichloro-2-methoxybenzoic acid
C8 H6 Cl2 O3
IWEDIXLBFLAXBO-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B],
J [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE

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: 2.10 Å
  • R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.323α = 90
b = 81.323β = 90
c = 159.282γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description