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- PDB-8oh5: Cryo-EM structure of the electron bifurcating transhydrogenase St... -

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Basic information

Entry
Database: PDB / ID: 8oh5
TitleCryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 2)
Components
  • Formate dehydrogenase-O, major subunit
  • NAD-dependent formate dehydrogenase gamma subunit
  • NAD-reducing hydrogenase subunit HoxF
KeywordsELECTRON TRANSPORT / flavin based Electron-bifurcation / transhydrogenases / anaerobic metabolism
Function / homology
Function and homology information


hydrogen dehydrogenase / hydrogen dehydrogenase activity / formate dehydrogenase / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / DNA binding / metal ion binding
Similarity search - Function
NADP-reducing hydrogenase subunit HndA / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Soluble ligand binding domain / SLBB domain / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. ...NADP-reducing hydrogenase subunit HndA / Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Soluble ligand binding domain / SLBB domain / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / 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 / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / FAD/NAD(P)-binding domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Pyridine nucleotide-disulphide oxidoreductase / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 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 / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-NDP / IRON/SULFUR CLUSTER / Formate dehydrogenase-O, major subunit / NAD-reducing hydrogenase subunit HoxF / NAD-dependent formate dehydrogenase gamma subunit
Similarity search - Component
Biological speciesSporomusa ovata DSM 2662 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsKumar, A. / Kremp, F. / Mueller, V. / Schuller, J.M.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101075992European Union
German Research Foundation (DFG)SCHU 3364/1-1 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Molecular architecture and electron transfer pathway of the Stn family transhydrogenase.
Authors: Anuj Kumar / Florian Kremp / Jennifer Roth / Sven A Freibert / Volker Müller / Jan M Schuller /
Abstract: The challenge of endergonic reduction of NADP using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood- ...The challenge of endergonic reduction of NADP using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Recently, an electron-bifurcating transhydrogenase with subunit compositions distinct from the well-characterized Nfn-type transhydrogenase was described: the Stn complex. Here, we present the single-particle cryo-EM structure of the Stn family transhydrogenase from the acetogenic bacterium Sporomusa ovata and functionally dissect its electron transfer pathway. Stn forms a tetramer consisting of functional heterotrimeric StnABC complexes. Our findings demonstrate that the StnAB subunits assume the structural and functional role of a bifurcating module, homologous to the HydBC core of the electron-bifurcating HydABC complex. Moreover, StnC contains a NuoG-like domain and a GltD-like NADPH binding domain that resembles the NfnB subunit of the NfnAB complex. However, in contrast to NfnB, StnC lost the ability to bifurcate electrons. Structural comparison allows us to describe how the same fold on one hand evolved bifurcation activity on its own while on the other hand combined with an associated bifurcating module, exemplifying modular evolution in anaerobic metabolism to produce activities critical for survival at the thermodynamic limit of life.
History
DepositionMar 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent formate dehydrogenase gamma subunit
B: NAD-reducing hydrogenase subunit HoxF
C: Formate dehydrogenase-O, major subunit
D: NAD-dependent formate dehydrogenase gamma subunit
E: NAD-reducing hydrogenase subunit HoxF
F: Formate dehydrogenase-O, major subunit
G: NAD-dependent formate dehydrogenase gamma subunit
H: NAD-reducing hydrogenase subunit HoxF
I: Formate dehydrogenase-O, major subunit
J: NAD-dependent formate dehydrogenase gamma subunit
K: NAD-reducing hydrogenase subunit HoxF
L: Formate dehydrogenase-O, major subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)861,76180
Polymers836,12712
Non-polymers25,63368
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area73470 Å2
ΔGint-1211 kcal/mol
Surface area293750 Å2
MethodPISA

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Components

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Protein , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
NAD-dependent formate dehydrogenase gamma subunit


Mass: 18973.877 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sporomusa ovata DSM 2662 (bacteria) / References: UniProt: A0A0U1KYW8
#2: Protein
NAD-reducing hydrogenase subunit HoxF


Mass: 63569.254 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sporomusa ovata DSM 2662 (bacteria) / References: UniProt: A0A0U1KYM9
#3: Protein
Formate dehydrogenase-O, major subunit


Mass: 126488.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sporomusa ovata DSM 2662 (bacteria) / References: UniProt: A0A0U1KYI6

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Non-polymers , 7 types, 68 molecules

#4: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#9: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#10: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / 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: Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata (state 2)
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 0.85 MDa / Experimental value: YES
Source (natural)Organism: Sporomusa ovata DSM 2662 (bacteria)
Buffer solutionpH: 8
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: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54596 / Symmetry type: POINT

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