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- PDB-7q4w: CryoEM structure of electron bifurcating Fe-Fe hydrogenase HydABC... -

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Basic information

Entry
Database: PDB / ID: 7q4w
TitleCryoEM structure of electron bifurcating Fe-Fe hydrogenase HydABC complex A. woodii in the oxidised state
Components(Iron hydrogenase ...) x 3
KeywordsELECTRON TRANSPORT / flavin-based electron bifurcating hydrogenase / FeFe hydrogenase / nicotine amide adenine dinucleotide / ferredoxin
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / metal ion binding
Similarity search - Function
: / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Soluble ligand binding domain ...: / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / Iron hydrogenase HydA1 / Iron hydrogenase HydB
Similarity search - Component
Biological speciesAcetobacterium woodii DSM 1030 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsKumar, A. / Saura, P. / Poeverlein, M.C. / Gamiz-Hernandez, A.P. / Kaila, V.R.I. / Mueller, V. / Schuller, J.M.
Funding support6items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3364/1-1
European Research Council (ERC)715311 (VRIK)
European Research Council (ERC)741791
Knut and Alice Wallenberg FoundationVRIK
German Research Foundation (DFG)SFB1078
Swedish Research Council016-07213
CitationJournal: J Am Chem Soc / Year: 2023
Title: Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC.
Authors: Alexander Katsyv / Anuj Kumar / Patricia Saura / Maximilian C Pöverlein / Sven A Freibert / Sven T Stripp / Surbhi Jain / Ana P Gamiz-Hernandez / Ville R I Kaila / Volker Müller / Jan M Schuller /
Abstract: Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO, but the molecular ...Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO, but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions is the electron-bifurcating [FeFe]-hydrogenase HydABC that reduces low-potential ferredoxins (Fd) by oxidizing hydrogen gas (H). By combining single-particle cryo-electron microscopy (cryoEM) under catalytic turnover conditions with site-directed mutagenesis experiments, functional studies, infrared spectroscopy, and molecular simulations, we show that HydABC from the acetogenic bacteria and employ a single flavin mononucleotide (FMN) cofactor to establish electron transfer pathways to the NAD(P) and Fd reduction sites by a mechanism that is fundamentally different from classical flavin-based electron bifurcation enzymes. By modulation of the NAD(P) binding affinity via reduction of a nearby iron-sulfur cluster, HydABC switches between the exergonic NAD(P) reduction and endergonic Fd reduction modes. Our combined findings suggest that the conformational dynamics establish a redox-driven kinetic gate that prevents the backflow of the electrons from the Fd reduction branch toward the FMN site, providing a basis for understanding general mechanistic principles of electron-bifurcating hydrogenases.
History
DepositionNov 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Structure summary / Category: entity / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron hydrogenase HydA1
B: Iron hydrogenase HydB
C: Iron hydrogenase HydC
E: Iron hydrogenase HydA1
F: Iron hydrogenase HydB
G: Iron hydrogenase HydC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,58428
Polymers261,9146
Non-polymers6,67022
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area23480 Å2
ΔGint-433 kcal/mol
Surface area99270 Å2
MethodPISA

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Components

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Iron hydrogenase ... , 3 types, 6 molecules AEBFCG

#1: Protein Iron hydrogenase HydA1


Mass: 63692.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acetobacterium woodii DSM 1030 (bacteria) / References: UniProt: H6LFG3, ferredoxin hydrogenase
#2: Protein Iron hydrogenase HydB


Mass: 50264.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acetobacterium woodii DSM 1030 (bacteria) / Strain: ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1 / References: UniProt: H6LFG4, ferredoxin hydrogenase
#3: Protein Iron hydrogenase HydC


Mass: 16999.689 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acetobacterium woodii DSM 1030 (bacteria) / References: ferredoxin hydrogenase

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Non-polymers , 4 types, 22 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Homodimer complex of HydABC trimer / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 350 kDa/nm / Experimental value: YES
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250709 / Symmetry type: POINT

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