4UR0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1126/science.1258118
  • Primary Citation of Related Structures:  
    4UQU, 4UR0, 4UR1, 4UR2, 4UR3

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA
A, B
464Sulfurospirillum multivoransMutation(s): 0 
EC: 1.97.1.8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BVQ
Query on BVQ

Download Ideal Coordinates CCD File 
E [auth A],
P [auth B]
NORPSEUDO-B12
C57 H82 Co N16 O14 P
XZMFKDUDYMLUGK-GVNDBXLGSA-M
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
N [auth B],
O [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
TCV
Query on TCV

Download Ideal Coordinates CCD File 
Q [auth B]1,1,2-trichloroethene
C2 H Cl3
XSTXAVWGXDQKEL-UHFFFAOYSA-N
BEN
Query on BEN

Download Ideal Coordinates CCD File 
F [auth A]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.956α = 90
b = 73.956β = 90
c = 185.421γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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: 2014-11-05
    Changes: Database references
  • Version 1.2: 2017-07-12
    Changes: Refinement description
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other