4UR0

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

• PDB DOI: https://doi.org/10.2210/pdb4UR0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurospirillum multivorans
• Mutation(s): No 


• Deposited: 2014-06-25 Released: 2014-10-15 
• Deposition Author(s): Bommer, M., Kunze, C., Fesseler, J., Schubert, T., Diekert, G., Dobbek, H.

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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 

Literature

Structural Basis for Organohalide Respiration.

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

(2014) Science 346: 455

• PubMed: 25278505 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109.43 kDa 
• Atom Count: 8,187 
• Modelled Residue Count: 887 
• Deposited Residue Count: 928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TETRACHLOROETHENE REDUCTIVE DEHALOGENASE CATALYTIC SUBUNIT PCEA	A, B	464	Sulfurospirillum multivorans	Mutation(s): 0  EC: 1.97.1.8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BVQ	E [auth A], P [auth B]	NORPSEUDO-B12 C57 H82 Co N16 O14 P XZMFKDUDYMLUGK-GVNDBXLGSA-M
SF4	C [auth A], D [auth A], N [auth B], O [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
TCV	Q [auth B]	1,1,2-trichloroethene C2 H Cl3 XSTXAVWGXDQKEL-UHFFFAOYSA-N
BEN	F [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
GOL	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 = 73.956	α = 90
b = 73.956	β = 90
c = 185.421	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Bommer, M., Kunze, C., Fesseler, J., Schubert, T., Diekert, G., Dobbek, H.

Revision History  

• 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