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Yorodumi- EMDB-16011: Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase H... -
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-Basic information
Entry | Database: EMDB / ID: EMD-16011 | |||||||||
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Title | Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state | |||||||||
Map data | Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state. | |||||||||
Sample |
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Function / homology | Function and homology information hydrogen dehydrogenase (NADP+) / hydrogen dehydrogenase (NADP+) activity / cellular anatomical entity / 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 ...hydrogen dehydrogenase (NADP+) / hydrogen dehydrogenase (NADP+) activity / cellular anatomical entity / 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 / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermoanaerobacter kivui (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
Authors | Kumar A / Schuller JM | |||||||||
Funding support | Germany, 1 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_16011.map.gz | 62.8 MB | EMDB map data format | |
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Header (meta data) | emd-16011-v30.xml emd-16011.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_16011.png | 92.4 KB | ||
Others | emd_16011_half_map_1.map.gz emd_16011_half_map_2.map.gz | 61.8 MB 61.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16011 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16011 | HTTPS FTP |
-Validation report
Summary document | emd_16011_validation.pdf.gz | 678.7 KB | Display | EMDB validaton report |
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Full document | emd_16011_full_validation.pdf.gz | 678.3 KB | Display | |
Data in XML | emd_16011_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_16011_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16011 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16011 | HTTPS FTP |
-Related structure data
Related structure data | 8bewMC 7q4vC 7q4wC 8a5eC 8a6tC 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_16011.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_16011_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_16011_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dimer of the trimeric HydABC complex
Entire | Name: Dimer of the trimeric HydABC complex |
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Components |
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-Supramolecule #1: Dimer of the trimeric HydABC complex
Supramolecule | Name: Dimer of the trimeric HydABC complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Thermoanaerobacter kivui (bacteria) |
-Macromolecule #1: Electron bifurcating hydrogenase subunit HydA1
Macromolecule | Name: Electron bifurcating hydrogenase subunit HydA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: hydrogen dehydrogenase (NADP+) |
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Source (natural) | Organism: Thermoanaerobacter kivui (bacteria) |
Molecular weight | Theoretical: 63.890727 KDa |
Sequence | String: 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 |
-Macromolecule #2: Electron bifurcating hydrogenase subunit HydB
Macromolecule | Name: Electron bifurcating hydrogenase subunit HydB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: hydrogen dehydrogenase (NADP+) |
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Source (natural) | Organism: Thermoanaerobacter kivui (bacteria) |
Molecular weight | Theoretical: 68.279047 KDa |
Sequence | String: 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 |
-Macromolecule #3: Electron bifurcating hydrogenase subunit HydC
Macromolecule | Name: Electron bifurcating hydrogenase subunit HydC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: hydrogen dehydrogenase (NADP+) |
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Source (natural) | Organism: Thermoanaerobacter kivui (bacteria) |
Molecular weight | Theoretical: 18.624678 KDa |
Sequence | String: MCNCCCKGSK DPRFEKVDEI LSKLANERGA LIAILQHVQH EFGYLPEDVI FYIASKTGIP ASKIYGVATF YAQFHLKPRG KYVIRVCLG TACHVKGANK ILAEFEKQLG IKAGETTSDL KFTLERVGCL GACGLAPTVM VNEKTYGKMT PEKVSEVLKE Y SDVEAAAS AQ |
-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: 6 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ChemComp-FES: |
-Macromolecule #6: FLAVIN MONONUCLEOTIDE
Macromolecule | Name: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 2 / Formula: FMN |
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Molecular weight | Theoretical: 456.344 Da |
Chemical component information | ChemComp-FMN: |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | JEOL CRYO ARM 200 |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 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 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130283 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |