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- EMDB-15166: Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase H... -

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Entry
Database: EMDB / ID: EMD-15166
TitleCryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state
Map dataCryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state
Sample
  • Complex: Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui
    • Protein or peptide: Iron hydrogenase HydA1
    • Protein or peptide: Iron hydrogenase HydB
    • Protein or peptide: Iron hydrogenase HydC
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER
  • Ligand: ZINC ION
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
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
Iron hydrogenase HydA1 / Iron hydrogenase HydB
Similarity search - Component
Biological speciesThermoanaerobacter kivui (bacteria) / Acetobacterium woodii DSM 1030 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKumar A / Saura P / Gamiz-Hernandez AP / Kaila VRI / Mueller V / Schuller JM
Funding support Germany, European Union, Sweden, 6 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3364/1-1 Germany
European Research Council (ERC)715311 (VRIK)European Union
European Research Council (ERC)741791European Union
Knut and Alice Wallenberg FoundationVRIK Sweden
German Research Foundation (DFG)SFB1078 Germany
Swedish Research Council016-07213 Sweden
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
DepositionJun 14, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15166.png

Downloads & links

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Map

FileDownload / File: emd_15166.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 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: 0.0534
Minimum - Maximum-1.2953877 - 1.9153503
Average (Standard dev.)0.0022648023 (±0.038498797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_15166_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_15166_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 : Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermo...

EntireName: Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui
Components
  • Complex: Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui
    • Protein or peptide: Iron hydrogenase HydA1
    • Protein or peptide: Iron hydrogenase HydB
    • Protein or peptide: Iron hydrogenase HydC
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER
  • Ligand: ZINC ION
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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Supramolecule #1: Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermo...

SupramoleculeName: Electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)
Molecular weightTheoretical: 348 KDa

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Macromolecule #1: Iron hydrogenase HydA1

MacromoleculeName: Iron hydrogenase HydA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 63.692887 KDa
SequenceString: MKEITFKING QEMIVPEGTT ILEAARMNNI DIPTLCYLKD INEIGACRMC LVEIAGARAL QAACVYPVAN GIEVLTNSPK VREARRVNL ELILSNHNRE CTTCIRSENC ELQTLATDLG VSDIPFEGEK SGKLIDDLST SVVRDESKCI LCKRCVSVCR D VQSVAVLG ...String:
MKEITFKING QEMIVPEGTT ILEAARMNNI DIPTLCYLKD INEIGACRMC LVEIAGARAL QAACVYPVAN GIEVLTNSPK VREARRVNL ELILSNHNRE CTTCIRSENC ELQTLATDLG VSDIPFEGEK SGKLIDDLST SVVRDESKCI LCKRCVSVCR D VQSVAVLG TVGRGFTSQV QPVFNKSLAD VGCINCGQCI INCPVGALKE KSDIQRVWDA IADPSKTVIV QTAPAVRAAL GE EFGYPMG TSVTGKMAAA LRRLGFDKVF DTDFGADVCI MEEGTELIGR VTNGGVLPMI TSCSPGWIKF IETYYPEAIP HLS SCKSPQ NITGALLKNH YAQTNNIDPK DMVVVSIMPC TAKKYEVQRE ELCTDGNADV DISITTRELA RMIKEARILF NKLP DEDFD DYYGESTGAA VIFGATGGVM EAAVRTVADV LNKKDIQEID YQIVRGVDGI KKASVEVTPD LTVNLVVAHG GANIR EVME QLKAGELADT HFIELMACPG GCVNGGGQPI VSAKDKMDID IRTERAKALY DEDANVLTYR KSHQNPSVIR LYEEYL EEP NSPKAHHILH TKYSAKPKLV

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Macromolecule #2: Iron hydrogenase HydB

MacromoleculeName: Iron hydrogenase HydB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 64.525965 KDa
SequenceString: MAYKRSQILI CGGTGCTSSG SMVLVKELKK ELVKHDILDE VEVVTTGCFG LCELGPVVIV YPEGTFYSRV EAADIPEMVE EHLVKGRPL DRLIYNEKGD GHHPLSINEL GFFKKQRRIA LANCGVINPE NIDEYIGFDG YLALEKVLLT MSPVDVINEV K ASGLRGRG ...String:
MAYKRSQILI CGGTGCTSSG SMVLVKELKK ELVKHDILDE VEVVTTGCFG LCELGPVVIV YPEGTFYSRV EAADIPEMVE EHLVKGRPL DRLIYNEKGD GHHPLSINEL GFFKKQRRIA LANCGVINPE NIDEYIGFDG YLALEKVLLT MSPVDVINEV K ASGLRGRG GGGFPTGLKW QFAHDAVSED GIKYVACNAD EGDPGAFMDR SVLEGDPHAV IEAMAIAGYA VGASKGYVYV RA EYPIAVN RLQIAIDQAK EYGILGENIF ETDFSFDLEI RLGAGAFVCG EETALMNSIE GKRGEPRPRP PFPANKGLFG KPT VLNNVE TYANIPKIIL NGAEWFASVG TEKSKGTKVF ALGGKINNTG LLEIPMGTTL REIIYEIGGG IPNGKAFKAA QTGG PSGGC LPESLLDTEI DYDNLIAAGS MMGSGGLIVM DEDNCMVDVA RFFLDFTQDE SCGKCPPCRI GTKRMLEILE RICDG KGVE GDIERLEELA VGIKSSALCG LGQTAPNPVL STIRFFRDEY EAHIRDKKCP AGVCKHLLDF KINADTCKGC GICAKK CPA DAISGEKKKP YNIDTSKCIK CGACIEACPF GSISKA

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Macromolecule #3: Iron hydrogenase HydC

MacromoleculeName: Iron hydrogenase HydC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase
Source (natural)Organism: Acetobacterium woodii DSM 1030 (bacteria)
Molecular weightTheoretical: 16.999689 KDa
SequenceString:
MAELIPVENL DVVKAIVAEH REVPGCLMQI LQETQLKYGY LPLELQGTIA DELGIPLTEV YGVATFYSQF TLKPKGKYKI GICLGTACY VRGSQAIIDK VNSVLGTQVG DTTEDGKWSV DATRCVGACG LAPVMMINEE VFGRLTVDEI PGILEKY

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Macromolecule #4: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 11 / 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: 3 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #6: 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER

MacromoleculeName: 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: HC1
Molecular weightTheoretical: 355.933 Da
Chemical component information

ChemComp-HC1:
2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 8 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #9: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 9 / Number of copies: 1 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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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: 7.6
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K2 SUMMIT (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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172189
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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