4RAS

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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This is version 1.2 of the entry. See complete history


Literature

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation.

Payne, K.A.Quezada, C.P.Fisher, K.Dunstan, M.S.Collins, F.A.Sjuts, H.Levy, C.Hay, S.Rigby, S.E.Leys, D.

(2015) Nature 517: 513-516

  • DOI: 10.1038/nature13901
  • Primary Citation of Related Structures:  
    4RAS

  • PubMed Abstract: 
  • Organohalide chemistry underpins many industrial and agricultural processes, and a large proportion of environmental pollutants are organohalides. Nevertheless, organohalide chemistry is not exclusively of anthropogenic origin, with natural abiotic and biological processes contributing to the global halide cycle ...

    Organohalide chemistry underpins many industrial and agricultural processes, and a large proportion of environmental pollutants are organohalides. Nevertheless, organohalide chemistry is not exclusively of anthropogenic origin, with natural abiotic and biological processes contributing to the global halide cycle. Reductive dehalogenases are responsible for biological dehalogenation in organohalide respiring bacteria, with substrates including polychlorinated biphenyls or dioxins. Reductive dehalogenases form a distinct subfamily of cobalamin (B12)-dependent enzymes that are usually membrane associated and oxygen sensitive, hindering detailed studies. Here we report the characterization of a soluble, oxygen-tolerant reductive dehalogenase and, by combining structure determination with EPR (electron paramagnetic resonance) spectroscopy and simulation, show that a direct interaction between the cobalamin cobalt and the substrate halogen underpins catalysis. In contrast to the carbon-cobalt bond chemistry catalysed by the other cobalamin-dependent subfamilies, we propose that reductive dehalogenases achieve reduction of the organohalide substrate via halogen-cobalt bond formation. This presents a new model in both organohalide and cobalamin (bio)chemistry that will guide future exploitation of these enzymes in bioremediation or biocatalysis.


    Organizational Affiliation

    Manchester Institute for Biotechnology, University of Manchester, Princess Street 131 M1 7DN Manchester, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxidoreductase, NAD-binding/iron-sulfur cluster-binding proteinA, B, C704Nitratireductor pacificus pht-3BMutation(s): 0 
Gene Names: NA2_14372
UniProt
Find proteins for K2MB66 (Nitratireductor pacificus pht-3B)
Explore K2MB66 
Go to UniProtKB:  K2MB66
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
F [auth A], K [auth B], P [auth C]COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], I [auth B], J [auth B], N [auth C], O [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A], L [auth B], Q [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A], M [auth B], R [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.34α = 90
b = 171.51β = 98.87
c = 109.02γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
MLPHAREphasing
REFMACrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Database references