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- EMDB-16878: Cryo-EM structure of the electron bifurcating transhydrogenase St... -

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Entry
Database: EMDB / ID: EMD-16878
TitleCryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 2)
Map dataSharp map
Sample
  • Complex: Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata (state 2)
    • Protein or peptide: NAD-dependent formate dehydrogenase gamma subunit
    • Protein or peptide: NAD-reducing hydrogenase subunit HoxF
    • Protein or peptide: Formate dehydrogenase-O, major subunit
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: ZINC ION
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Keywordsflavin based Electron-bifurcation / transhydrogenases / anaerobic metabolism / ELECTRON TRANSPORT
Function / homology
Function and homology information


hydrogen dehydrogenase / hydrogen dehydrogenase activity / formate dehydrogenase / 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, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKumar A / Kremp F / Mueller V / Schuller JM
Funding supportEuropean Union, Germany, 2 items
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, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16878.png

Downloads & links

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Map

FileDownload / File: emd_16878.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.164
Minimum - Maximum-1.0963533 - 1.7487273
Average (Standard dev.)0.00088260404 (±0.054045204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Non-sharpened map

Fileemd_16878_additional_1.map
AnnotationNon-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_16878_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 A

Fileemd_16878_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the electron bifurcating trans-hydrogenase S...

EntireName: Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata (state 2)
Components
  • Complex: Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata (state 2)
    • Protein or peptide: NAD-dependent formate dehydrogenase gamma subunit
    • Protein or peptide: NAD-reducing hydrogenase subunit HoxF
    • Protein or peptide: Formate dehydrogenase-O, major subunit
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: ZINC ION
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: Cryo-EM structure of the electron bifurcating trans-hydrogenase S...

SupramoleculeName: Cryo-EM structure of the electron bifurcating trans-hydrogenase StnABC complex from Sporomusa Ovata (state 2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Sporomusa ovata DSM 2662 (bacteria)
Molecular weightTheoretical: 850 KDa

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Macromolecule #1: NAD-dependent formate dehydrogenase gamma subunit

MacromoleculeName: NAD-dependent formate dehydrogenase gamma subunit / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sporomusa ovata DSM 2662 (bacteria)
Molecular weightTheoretical: 18.973877 KDa
SequenceString:
MCNSCEKELE TKFPADKIDL TLLEPVFKEY AGKAGSIIGI LQKTQEIYGY LPLAALQAIA DNTDNKRAKI YGIATFYSQF RLNPVGKYV ILQCQGTACH VLGSKAIGSA ICDELGITPG QTTADGLFTL EDVACLGCCS LAPVIMINGE AYGKLTPTSV R KILQDIAE AEKGGVVSEG

UniProtKB: NAD-dependent formate dehydrogenase gamma subunit

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Macromolecule #2: NAD-reducing hydrogenase subunit HoxF

MacromoleculeName: NAD-reducing hydrogenase subunit HoxF / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sporomusa ovata DSM 2662 (bacteria)
Molecular weightTheoretical: 63.569254 KDa
SequenceString: MKVRVGLGSC GIAAGGRKVM DRLAQEIKNH GKEIELLPTG CIGMCFYEPI VDVFDGDKVY SYANVTADMA TEIFNSHIIG GQPLTQYIV STTEKPYTIL AKQVRIALRN CGVIDPENVD EYKANDGYKA LSKALKEMTP EEVIEEIKVA GLRGRGGAGF P TWFKWNAA ...String:
MKVRVGLGSC GIAAGGRKVM DRLAQEIKNH GKEIELLPTG CIGMCFYEPI VDVFDGDKVY SYANVTADMA TEIFNSHIIG GQPLTQYIV STTEKPYTIL AKQVRIALRN CGVIDPENVD EYKANDGYKA LSKALKEMTP EEVIEEIKVA GLRGRGGAGF P TWFKWNAA RQSKGEIKYV VCNADEGDPG AFMDRSVLEG DPHALLEGMA ICGYAIGANE GHIYCRAEYP LAIKRLEIAI AD AKQRNLL GKNIMGTNFS FDMKIKKGAG AFVCGEETAL IASLEGERGM PRLKPPFPAQ SGFWGKPTNI NNVETFANVP WIM YNGGSA YAAYGTEKSK GTKVFALAGK IKNGGLVEVP MGMSLREVIY DIGGGILNDR EFKAVQMGGP SGGCIPKQLL DTPV DYDSI NKTGAIMGSG GMIVMDETTC MVDMARFFLD FTVKESCGKC IYCRIGTKRM LEILERITTG EGREGDIEEL EELSI SIKD GSLCGLGQTA PNPVLTTIRY FRDEYEAHIR DKKCPAKSCK PLLTYTINQD NCKGCTLCAQ KCPVQAITGE KKKPHV IDQ ALCTKCGNCA SVCRLDAVCI E

UniProtKB: NAD-reducing hydrogenase subunit HoxF

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Macromolecule #3: Formate dehydrogenase-O, major subunit

MacromoleculeName: Formate dehydrogenase-O, major subunit / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sporomusa ovata DSM 2662 (bacteria)
Molecular weightTheoretical: 126.488734 KDa
SequenceString: MSKISINING RELVVSAGQT ILQAAAEHGI EIPHLCHDER IQPYGACGLC VVEVEGSPKL VRSCATSVQN GQVIRTDTSR TVVARKTAL QLLASDHRGD CRPPCMLACP AQTDCQGYVG LIANGQYEEA LKLIKDKMPI PASIGKICPH PCETACRREL V EEPISIAQ ...String:
MSKISINING RELVVSAGQT ILQAAAEHGI EIPHLCHDER IQPYGACGLC VVEVEGSPKL VRSCATSVQN GQVIRTDTSR TVVARKTAL QLLASDHRGD CRPPCMLACP AQTDCQGYVG LIANGQYEEA LKLIKDKMPI PASIGKICPH PCETACRREL V EEPISIAQ LKSFVAEVDL NGNQYQPPMK PATGKKVAVV GAGPAGLTAA YFLARDGHKV VIYEAMPHPG GMLRYGIPQY RL DKALLDA EVALMTKMGI EIIYNTKIGD DVSLDYLHDN YDAVFLGIGS WQSQGLRCKG EDMEGVLGGI DFLREVTMNS NIT LGGKVL VVGGGNTAMD VARTSKRLGA EEVTIIYRRT IDEMPAEKIE IHEAQEEGVK FQLLVAPVEV LGENGHAKAL KCEI MRLGE PDASGRRKPE PTGETVVYEA DRIIAAIGQK TVIGNIKDIA TDKSGNIIVN GGAFTTNRDK VFAGGDAVTG PKIAI DAIA QGKNAAQVID SYLNGCLVPH ADSQYFTQKD ITAADLADRA KAPRVSLTVE DAEVRNKSFM QVAKTFTEEE ALRESK RCL ECGCRDYFEC QLIKYIQDYD VSTEKDSQVE CHKTTEFDNH PFIERNPDKC VLCGLCVRVC DEVVGATAIG LVGRGFD SV IMPEFKLPLS ETACISCGQC VDVCPTGACM EKQVSYKQIP ANMDSMASVC GYCGVGCNVN IEYKGDVVFR VTPDRVND D GWLCQRGKFG LGHANDKARL TAPVIKRNGQ FVKVDWNEAN LEVVKRLQAV VAAYGKDSIG VVVSPRLTNE ELFLAGKLA DAVNTTIKTS YSVDGGSGLG SVLGYDASTN SFAELDNSDF VLTLGKVKEN HPVLDFKIRL SGVCSVAWPQ SLANTADMKV FLKALLNLG VDENKVAEKT EGFAELKASL ADVKVSEEIQ ALAQKYAKAA KPLIVIDEDT VSAEAVKLMA YAAVITGKIG A AYRGIILV RTKNNTQGAV DMGFVMPVSA VAQGIESGKI KALVVIGEDP AAYPQESALL QKLSFLVVYD MFMTKTATAA DM VVPLVSS AEVNGTYTRS DRRIQAVRAA IQPKTGKATL QILIETLKSL GIKYDTIADV RAAIASEVSN YAGMDAADFG TTV YWPNNK NVLYTDGFAT EGQKAILAAV GDVPVFVEKK KYDSVEMNFV NGRQSL

UniProtKB: Formate dehydrogenase-O, major subunit

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Macromolecule #4: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 4 / Number of copies: 12 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 4 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 36 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #8: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 8 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

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Macromolecule #9: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 9 / Number of copies: 4 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM / Flavin adenine dinucleotide

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Macromolecule #10: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 10 / Number of copies: 4 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

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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: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54596

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