4UR0

Crystal structure of the PCE reductive dehalogenase from S. multivorans in complex with trichloroethene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.798 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Organohalide Respiration.

Bommer, M.Kunze, C.Fesseler, J.Schubert, T.Diekert, G.Dobbek, H.

(2014) Science 346: 455

  • DOI: 10.1126/science.1258118
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Organohalide-respiring microorganisms can use a variety of persistent pollutants, including trichloroethene (TCE), as terminal electron acceptors. The final two-electron transfer step in organohalide respiration is catalyzed by reductive dehalogenase ...

    Organohalide-respiring microorganisms can use a variety of persistent pollutants, including trichloroethene (TCE), as terminal electron acceptors. The final two-electron transfer step in organohalide respiration is catalyzed by reductive dehalogenases. Here we report the x-ray crystal structure of PceA, an archetypal dehalogenase from Sulfurospirillum multivorans, as well as structures of PceA in complex with TCE and product analogs. The active site harbors a deeply buried norpseudo-B12 cofactor within a nitroreductase fold, also found in a mammalian B12 chaperone. The structures of PceA reveal how a cobalamin supports a reductive haloelimination exploiting a conserved B12-binding scaffold capped by a highly variable substrate-capturing region.


    Organizational Affiliation

    Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA
A, B
464Sulfurospirillum multivorans DSM 12446Gene Names: pceA
Find proteins for W6EQP0 (Sulfurospirillum multivorans DSM 12446)
Go to UniProtKB:  W6EQP0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
BVQ
Query on BVQ

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Download CCD File 
A, B
NORPSEUDO-B12
C57 H82 Co N16 O14 P
XZMFKDUDYMLUGK-GVNDBXLGSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TCV
Query on TCV

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Download CCD File 
B
1,1,2-trichloroethene
C2 H Cl3
XSTXAVWGXDQKEL-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

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Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.798 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.136 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 73.956α = 90.00
b = 73.956β = 90.00
c = 185.421γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-11-05
    Type: Database references
  • Version 1.2: 2017-07-12
    Type: Refinement description