+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13818 | |||||||||||||||||||||
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Title | Electron bifurcating hydrogenase - HydABC from A. woodii | |||||||||||||||||||||
Map data | Single-Particle Cryo-EM Reconstruction of the Electron Bifurcating Hydrogenase HydABC (Processed on RELION - non-sharpened map) | |||||||||||||||||||||
Sample |
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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 | |||||||||||||||||||||
Biological species | Acetobacterium woodii DSM 1030 (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||||||||||||||
Authors | Katsyv A / Kumar A / Saura P / Poeverlein MC / Freibert SA / Stripp S / Jain S / Gamiz-Hernandez AP / Kaila VRI / Mueller V / Schuller JM | |||||||||||||||||||||
Funding support | European Union, 6 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13818.map.gz | 22.9 MB | EMDB map data format | |
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Header (meta data) | emd-13818-v30.xml emd-13818.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_13818.png | 77.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13818 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13818 | HTTPS FTP |
-Validation report
Summary document | emd_13818_validation.pdf.gz | 382.3 KB | Display | EMDB validaton report |
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Full document | emd_13818_full_validation.pdf.gz | 381.8 KB | Display | |
Data in XML | emd_13818_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | emd_13818_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13818 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13818 | HTTPS FTP |
-Related structure data
Related structure data | 7q4vMC 7q4wC 8a5eC 8a6tC 8bewC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13818.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Single-Particle Cryo-EM Reconstruction of the Electron Bifurcating Hydrogenase HydABC (Processed on RELION - non-sharpened map) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Homodimer complex of HydABC trimer
Entire | Name: Homodimer complex of HydABC trimer |
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Components |
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-Supramolecule #1: Homodimer complex of HydABC trimer
Supramolecule | Name: Homodimer complex of HydABC trimer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Acetobacterium woodii DSM 1030 (bacteria) |
Molecular weight | Theoretical: 300 kDa/nm |
-Macromolecule #1: Iron hydrogenase HydA1
Macromolecule | Name: Iron hydrogenase HydA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase |
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Source (natural) | Organism: Acetobacterium woodii DSM 1030 (bacteria) |
Molecular weight | Theoretical: 63.692887 KDa |
Sequence | String: 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 |
-Macromolecule #2: Iron hydrogenase HydB
Macromolecule | Name: Iron hydrogenase HydB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase |
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Source (natural) | Organism: Acetobacterium woodii DSM 1030 (bacteria) |
Molecular weight | Theoretical: 64.525965 KDa |
Sequence | String: 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 |
-Macromolecule #3: Iron hydrogenase HydC
Macromolecule | Name: Iron hydrogenase HydC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase |
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Source (natural) | Organism: Acetobacterium woodii DSM 1030 (bacteria) |
Molecular weight | Theoretical: 16.999689 KDa |
Sequence | String: MAELIPVENL DVVKAIVAEH REVPGCLMQI LQETQLKYGY LPLELQGTIA DELGIPLTEV YGVATFYSQF TLKPKGKYKI GICLGTACY VRGSQAIIDK VNSVLGTQVG DTTEDGKWSV DATRCVGACG LAPVMMINEE VFGRLTVDEI PGILEKY |
-Macromolecule #4: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 4 / Number of copies: 14 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER
Macromolecule | Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 5 / Number of copies: 5 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ChemComp-FES: |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #7: FLAVIN MONONUCLEOTIDE
Macromolecule | Name: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 2 / Formula: FMN |
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Molecular weight | Theoretical: 456.344 Da |
Chemical component information | ChemComp-FMN: |
-Macromolecule #8: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 8 / Number of copies: 1 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 559245 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |