5MA2

PCE reductive dehalogenase from S. multivorans in complex with 4-iodophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1038/ncomms15858
  • Primary Citation of Related Structures:  
    5M2G, 5M8U, 5M8W, 5M8X, 5M8Y, 5M8Z, 5M90, 5M91, 5M92, 5MA0, 5MA1, 5MA2, 5MAA

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetrachloroethene reductive dehalogenase catalytically active subunit
A, B
464Sulfurospirillum multivoransMutation(s): 0 
EC: 1.21.99.5
UniProt
Find proteins for O68252 (Sulfurospirillum multivorans)
Explore O68252 
Go to UniProtKB:  O68252
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68252
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BVQ
Query on BVQ

Download Ideal Coordinates CCD File 
E [auth A],
Q [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],
O [auth B],
P [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
IOL
Query on IOL

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
T [auth B]
U [auth B]
K [auth A],
L [auth A],
M [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
4-IODOPHENOL
C6 H5 I O
VSMDINRNYYEDRN-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
N [auth A],
Y [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
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]
R [auth B]
G [auth A],
H [auth A],
I [auth A],
J [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: 1.88 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.765α = 90
b = 73.765β = 90
c = 184.711γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description