4UQU | pdb_00004uqu

Crystal structure of the tetrachloroethene reductive dehalogenase from Sulfurospirillum multivorans

PDB DOI: https://doi.org/10.2210/pdb4UQU/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.183 (Depositor), 0.183 (DCC)
R-Value Work:
0.152 (Depositor), 0.154 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

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

PubMed: 25278505 Search on PubMed
DOI: https://doi.org/10.1126/science.1258118
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 109.07 kDa
Atom Count: 7,983
Modeled Residue Count: 878
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BVQ Query on BVQ Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain E [auth A]	E [auth A], O [auth B]	NORPSEUDO-B12 C₅₇ H₈₂ Co N₁₆ O₁₄ P XZMFKDUDYMLUGK-GVNDBXLGSA-M		Interactions Focus chain E [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain O [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], M [auth B], N [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain M [auth B] Focus chain N [auth B]
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], L [auth A]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.183 (Depositor), 0.183 (DCC)
R-Value Work: 0.152 (Depositor), 0.154 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.143	α = 90
b = 73.143	β = 90
c = 183.093	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

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