Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 110.44 kDa 
• Atom Count: 7904 
• Modelled Residue Count: 862 
• Deposited Residue Count: 928 
• Unique protein chains: 1

5M92

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

• DOI: 10.2210/pdb5M92/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurospirillum multivorans DSM 12446
• Mutation(s): No 


• Deposited: 2016-10-31 Released: 2017-07-12 
• Deposition Author(s): Kunze, C., Bommer, M., Hagen, W.R., Uksa, M., Dobbek, H., Schubert, T., Diekert, G.
• Funding Organization(s): German Research Foundation

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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 

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

• PubMed: 28671181 
• DOI: 10.1038/ncomms15858
• Primary Citation of Related Structures:  
  5M2G, 5M8Y, 5M8X, 5M8Z, 5M92, 5M91, 5MAA, 5MA2, 5MA1, 5MA0, 5M8U, 5M8W, 5M90


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrachloroethene reductive dehalogenase catalytic subunit PceA	A, B	464	Sulfurospirillum multivorans DSM 12446	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BVQ (Subject of Investigation/LOI)	E [auth A], S [auth B]	NORPSEUDO-B12 C57 H82 Co N16 O14 P XZMFKDUDYMLUGK-GVNDBXLGSA-M
SF4	C [auth A], D [auth A], Q [auth B], R [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
Y8I (Subject of Investigation/LOI)	N [auth A], O [auth A], V [auth B], W [auth B]	2,4-bis(bromanyl)phenol C6 H4 Br2 O FAXWFCTVSHEODL-UHFFFAOYSA-N
BEN	F [auth A], M [auth A], U [auth B]	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], T [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR	P [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

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 = 73.944	α = 90
b = 73.944	β = 90
c = 185.109	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-31 
• Released Date: 2017-07-12 
Deposition Author(s): Kunze, C., Bommer, M., Hagen, W.R., Uksa, M., Dobbek, H., Schubert, T., Diekert, G.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	FOR1530
German Research Foundation	Germany	SFB1078

Revision History  

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