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- PDB-8q4h: a membrane-bound menaquinol:organohalide oxidoreductase complex R... -

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Basic information

Entry
Database: PDB / ID: 8q4h
Titlea membrane-bound menaquinol:organohalide oxidoreductase complex RDH complex
Components
  • Probable tetrachloroethene reductive dehalogenase membrane anchor protein
  • Tetrachloroethene reductive dehalogenase
KeywordsELECTRON TRANSPORT / RDH menaquinol:organohalide oxidoreductase
Function / homology
Function and homology information


tetrachloroethene reductive dehalogenase / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / plasma membrane
Similarity search - Function
TAT (twin-arginine translocation) pathway signal sequence / 4Fe-4S double cluster binding domain / Reductive dehalogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
CO-METHYLCOBALAMIN / (~{Z})-1,2-bis(chloranyl)ethene / MENAQUINONE-7 / IRON/SULFUR CLUSTER / Probable tetrachloroethene reductive dehalogenase membrane anchor protein / Tetrachloroethene reductive dehalogenase
Similarity search - Component
Biological speciesDesulfitobacterium hafniense TCE1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsDongchun, N. / Ekundayo, B. / Henning, S. / Julien, M. / Holliger, C. / Cimmino, L.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_177195 Switzerland
Swiss National Science FoundationIZLCZ0_206089 Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: Structure of a membrane-bound menaquinol:organohalide oxidoreductase.
Authors: Lorenzo Cimmino / Américo G Duarte / Dongchun Ni / Babatunde E Ekundayo / Inês A C Pereira / Henning Stahlberg / Christof Holliger / Julien Maillard /
Abstract: Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory ...Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohalides as substrates and contribute to energy conservation. Here, we present the structure of a menaquinol:organohalide oxidoreductase obtained by cryo-EM. The membrane-bound protein was isolated from Desulfitobacterium hafniense strain TCE1 as a PceAB complex catalysing the dechlorination of tetrachloroethene. Two catalytic PceA subunits are anchored to the membrane by two small integral membrane PceB subunits. The structure reveals two menaquinone molecules bound at the interface of the two different subunits, which are the starting point of a chain of redox cofactors for electron transfer to the active site. In this work, the structure elucidates how energy is conserved during organohalide respiration in menaquinone-dependent organohalide-respiring bacteria.
History
DepositionAug 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetrachloroethene reductive dehalogenase
B: Tetrachloroethene reductive dehalogenase
C: Probable tetrachloroethene reductive dehalogenase membrane anchor protein
D: Probable tetrachloroethene reductive dehalogenase membrane anchor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,08314
Polymers133,4964
Non-polymers5,58710
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Tetrachloroethene reductive dehalogenase


Mass: 56620.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: (COB)(SF4)(SF4)(MQ7)
Source: (natural) Desulfitobacterium hafniense TCE1 (bacteria)
References: UniProt: Q8GJ31
#2: Protein Probable tetrachloroethene reductive dehalogenase membrane anchor protein


Mass: 10126.991 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Desulfitobacterium hafniense TCE1 (bacteria)
References: UniProt: Q8GJ30

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Non-polymers , 5 types, 24 molecules

#3: Chemical ChemComp-JYF / (~{Z})-1,2-bis(chloranyl)ethene


Mass: 96.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2Cl2
#4: Chemical ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H91CoN13O14P
#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H64O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: a membrane-bound menaquinol:organohalide oxidoreductase
Type: COMPLEX / Details: PceA2B2 / Entity ID: #2 / Source: NATURAL
Molecular weightValue: 130 kDa/nm / Experimental value: YES
Source (natural)Organism: Desulfitobacterium hafniense TCE1 (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34078 / Symmetry type: POINT

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