5M92

PCE reductive dehalogenase from S. multivorans in complex with 2,4-dibromophenol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer.

Kunze, C., Bommer, M., Hagen, W.R., Uksa, M., Dobbek, H., Schubert, T., Diekert, G.

(2017) Nat Commun 8: 15858-15858

  • DOI: 10.1038/ncomms15858
  • Primary Citation of Related Structures:  
    5MAA, 5MA2, 5MA1, 5MA0, 5M8U, 5M8W, 5M90, 5M2G, 5M8Y, 5M8X

  • PubMed Abstract: 

    • The capacity of metal-containing porphyrinoids to mediate reductive dehalogenation is implemented in cobamide-containing reductive dehalogenases (RDases), which serve as terminal reductases in organohalide-respiring microbes. RDases allow for the exploitation of halogenated compounds as electron acceptors ...

    The capacity of metal-containing porphyrinoids to mediate reductive dehalogenation is implemented in cobamide-containing reductive dehalogenases (RDases), which serve as terminal reductases in organohalide-respiring microbes. RDases allow for the exploitation of halogenated compounds as electron acceptors. Their reaction mechanism is under debate. Here we report on substrate-enzyme interactions in a tetrachloroethene RDase (PceA) that also converts aryl halides. The shape of PceA's highly apolar active site directs binding of bromophenols at some distance from the cobalt and with the hydroxyl substituent towards the metal. A close cobalt-substrate interaction is not observed by electron paramagnetic resonance spectroscopy. Nonetheless, a halogen substituent para to the hydroxyl group is reductively eliminated and the path of the leaving halide is traced in the structure. Based on these findings, an enzymatic mechanism relying on a long-range electron transfer is concluded, which is without parallel in vitamin B 12 -dependent biochemistry and represents an effective mode of RDase catalysis.

    Organizational Affiliation: 

    Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, Jena D-07743, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tetrachloroethene reductive dehalogenase catalytic subunit PceAA, B464Sulfurospirillum multivorans DSM 12446Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BVQ
Query on BVQ
Download Ideal Coordinates CCD File 
 E [auth A], S [auth B]NORPSEUDO-B12
C57 H82 Co N16 O14 P
XZMFKDUDYMLUGK-GVNDBXLGSA-M		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
 C [auth A], D [auth A], Q [auth B], R [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
Y8I
Query on Y8I
Download Ideal Coordinates CCD File 
 N [auth A], O [auth A], V [auth B], W [auth B]2,4-bis(bromanyl)phenol
C6 H4 Br2 O
FAXWFCTVSHEODL-UHFFFAOYSA-N		 Ligand Interaction
BEN
Query on BEN
Download Ideal Coordinates CCD File 
 F [auth A], M [auth A], U [auth B]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
 G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], T [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
BR
Query on BR
Download Ideal Coordinates CCD File 
 P [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.944α = 90
b = 73.944β = 90
c = 185.109γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1530
German Research FoundationGermanySFB1078

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release