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- EMDB-16011: Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase H... -

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Entry
Database: EMDB / ID: EMD-16011
TitleCryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state
Map dataCryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state.
Sample
  • Complex: Dimer of the trimeric HydABC complex
    • Protein or peptide: Electron bifurcating hydrogenase subunit HydA1
    • Protein or peptide: Electron bifurcating hydrogenase subunit HydB
    • Protein or peptide: Electron bifurcating hydrogenase subunit HydC
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: ZINC ION
KeywordsBioenergetics / Acetogenesis / Flavin-based electron bifurcation / [FeFe]-hydrogenase / molecular simulations / ELECTRON TRANSPORT
Function / homology
Function and homology information


hydrogen dehydrogenase (NADP+) / hydrogen dehydrogenase (NADP+) activity / ferredoxin hydrogenase activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding / membrane
Similarity search - Function
: / NADP-reducing hydrogenase subunit HndA / 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 ...: / NADP-reducing hydrogenase subunit HndA / 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 / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / 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 / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Electron bifurcating hydrogenase subunit HydA1 / Electron bifurcating hydrogenase subunit HydB / Electron bifurcating hydrogenase subunit HydC
Similarity search - Component
Biological speciesThermoanaerobacter kivui (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsKumar A / Schuller JM
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3364/1-1 Germany
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
DepositionOct 22, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16011.png

Downloads & links

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Map

FileDownload / File: emd_16011.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 280 pix.
= 243.6 Å		0.87 Å/pix.
x 280 pix.
= 243.6 Å		0.87 Å/pix.
x 280 pix.
= 243.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.63560593 - 2.1561034
Average (Standard dev.)0.0024341163 (±0.028507354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 243.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_16011_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_16011_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of the trimeric HydABC complex

EntireName: Dimer of the trimeric HydABC complex
Components
  • Complex: Dimer of the trimeric HydABC complex
    • Protein or peptide: Electron bifurcating hydrogenase subunit HydA1
    • Protein or peptide: Electron bifurcating hydrogenase subunit HydB
    • Protein or peptide: Electron bifurcating hydrogenase subunit HydC
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: ZINC ION

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Supramolecule #1: Dimer of the trimeric HydABC complex

SupramoleculeName: Dimer of the trimeric HydABC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)

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Macromolecule #1: Electron bifurcating hydrogenase subunit HydA1

MacromoleculeName: Electron bifurcating hydrogenase subunit HydA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: hydrogen dehydrogenase (NADP+)
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)
Molecular weightTheoretical: 63.890727 KDa
SequenceString: MNMVMLTIDG KQVQVEKGTT IKKAAEKLGI EIPGLCDDND LKPFGACRLC VVEDARGNLV ASCHTPVREG MVVKTNSPKV LKARRVILE LLLSSHNADC FECDKNLHCK LQKYAYELNI RNIRFKGEKR NYEIKDNGPI YYDPNKCILC GKCVRICEEV Q HICAIDFA ...String:
MNMVMLTIDG KQVQVEKGTT IKKAAEKLGI EIPGLCDDND LKPFGACRLC VVEDARGNLV ASCHTPVREG MVVKTNSPKV LKARRVILE LLLSSHNADC FECDKNLHCK LQKYAYELNI RNIRFKGEKR NYEIKDNGPI YYDPNKCILC GKCVRICEEV Q HICAIDFA SRGFKAYIST PFEKPLLESD CIFCGQCVRV CPTGALAEKT DIERIYEAIS DPNKVVVVQV APAVRVALGE EF GLEPGEI VTGKMVAALK RLGFDKVFDT QFAADMTIVE ETAELVERLE KGENFPMFTS CCPSWILAVE KFYPELIPNI STA RSPQQI FGAIAKNYYA KKIGVARENM FVVSVMPCIG KKFEATRPEF NNDVDAVLTT RELARMIKES GIDFIKLEEE NFDS PLGES TGAAAIFGVT GGVMEAALRT AYSIMTGEEL EGDKIEFTAV RGLEGIKEAE VDIKGKKVRI AIANGIGNAK KLIEK IKSG ETKYDFVEVM ACPGGCMSGG GQPYTDDPEF RKKRMEGIYK NDRNLPKRKS HENEEVKKVY EEYYEKPCGP KAHEEL HTH YHSRKKEY

UniProtKB: Electron bifurcating hydrogenase subunit HydA1

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Macromolecule #2: Electron bifurcating hydrogenase subunit HydB

MacromoleculeName: Electron bifurcating hydrogenase subunit HydB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: hydrogen dehydrogenase (NADP+)
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)
Molecular weightTheoretical: 68.279047 KDa
SequenceString: MVKLKSIQEL ENLREKIKEA KKKEKIVIRI CGGTGCRASG SLAVRDELVK VLKREGFANV DVNLSSDCLE NTSEVHVKMT GCQGFCAQG PLMTIEPLGV FYVGVKPEDV EEIVEKSIKK NEIIERLLYH DPATGKTYVK RDENPFYAKQ TRLVLKHCGT V DPASVYDY ...String:
MVKLKSIQEL ENLREKIKEA KKKEKIVIRI CGGTGCRASG SLAVRDELVK VLKREGFANV DVNLSSDCLE NTSEVHVKMT GCQGFCAQG PLMTIEPLGV FYVGVKPEDV EEIVEKSIKK NEIIERLLYH DPATGKTYVK RDENPFYAKQ TRLVLKHCGT V DPASVYDY IAEGGYSAIA KALTMDRKQI IDEVIKSGLR GRGGAGFPTG EKWLGAYKNQ SPKKYIICNG DEGDPGAFMD RS VMEGDPH KVIEGMMIGA YAIGSDEGYI YVRAEYPLAV QMLRKAIEEC EKLGLLGDNI LGTGFSFRLH VREGAGAFVC GES TALTYS IEGKRGMPRV RPPRTNECGL WEMPTVLNNV ETFACIPEII LNGGEWFASI GTPTSTGTKI FALSGKVNRT GLVE VPMGL KLRELIFDIG GGIANNKKFK AVQLGGPSGG CVPESQLDLP IDFDSLSKAG AIMGSGGVVV VDEDTCMVDF AKFFT NFIV EESCGKCIPC REGNKKMLEI LERITEGKGK EGDIELLEEL GDVIISASLC GLGKTAPNPV LSTIKHFRDE YEAHIR DKK CPAGACQALA AYKIDPGKCI GCGKCVKVCP VGAISGEKKK PHVIDQSKCI KCGACAENCP KGAIYKG

UniProtKB: Electron bifurcating hydrogenase subunit HydB

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Macromolecule #3: Electron bifurcating hydrogenase subunit HydC

MacromoleculeName: Electron bifurcating hydrogenase subunit HydC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: hydrogen dehydrogenase (NADP+)
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)
Molecular weightTheoretical: 18.624678 KDa
SequenceString:
MCNCCCKGSK DPRFEKVDEI LSKLANERGA LIAILQHVQH EFGYLPEDVI FYIASKTGIP ASKIYGVATF YAQFHLKPRG KYVIRVCLG TACHVKGANK ILAEFEKQLG IKAGETTSDL KFTLERVGCL GACGLAPTVM VNEKTYGKMT PEKVSEVLKE Y SDVEAAAS AQ

UniProtKB: Electron bifurcating hydrogenase subunit HydC

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Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 14 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 5 / Number of copies: 6 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #6: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130283
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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