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- EMDB-14169: Cryo-EM structure of Hydrogen-dependent CO2 reductase. -

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Basic information

Entry
Database: EMDB / ID: EMD-14169
TitleCryo-EM structure of Hydrogen-dependent CO2 reductase.
Map data3.4 Angstrom Cryo-EM structure of HDCR complex. The data was processed using cryosparc software.
Sample
  • Complex: Hydrogen-dependent CO2 reductase (HDCR) complex with iron-sulphur clusters and the H-cluster.
    • Protein or peptide: Hydrogen dependent carbon dioxide reductase subunit HycB3
    • Protein or peptide: Hydrogen dependent carbon dioxide reductase subunit HycB4
    • Protein or peptide: Hydrogen dependent carbon dioxide reductase subunit HydA2
    • Protein or peptide: Hydrogen dependent carbon dioxide reductase subunit FdhF
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
Function / homology
Function and homology information


formate dehydrogenase / formate metabolic process / ferredoxin hydrogenase / formate dehydrogenase (NAD+) activity / ferredoxin hydrogenase activity / Oxidoreductases / molybdopterin cofactor binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...formate dehydrogenase / formate metabolic process / ferredoxin hydrogenase / formate dehydrogenase (NAD+) activity / ferredoxin hydrogenase activity / Oxidoreductases / molybdopterin cofactor binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding
Similarity search - Function
4Fe-4S binding domain / Formate dehydrogenase H, molybdopterin-binding domain / 4Fe-4S binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. ...4Fe-4S binding domain / Formate dehydrogenase H, molybdopterin-binding domain / 4Fe-4S binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / 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 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 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
Similarity search - Domain/homology
Hydrogen dependent carbon dioxide reductase subunit HydA2 / Hydrogen dependent carbon dioxide reductase subunit HycB3 / Hydrogen dependent carbon dioxide reductase subunit FdhF / Hydrogen dependent carbon dioxide reductase subunit HycB4
Similarity search - Component
Biological speciesThermoanaerobacter kivui LKT-1 (bacteria) / Thermoanaerobacter kivui (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDietrich HM / Righetto RD / Kumar A / Wietrzynski W / Schuller SK / Trischler R / Wagner J / Schwarz FM / Engel BD / Mueller V / Schuller JM
Funding support Germany, European Union, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3364/1-1 Germany
European Research Council (ERC)741791European Union
German Research Foundation (DFG)FOR 2092 Germany
Alexander von Humboldt Foundation Germany
German Research Foundation (DFG)20016/446 Germany
CitationJournal: Nature / Year: 2022
Title: Membrane-anchored HDCR nanowires drive hydrogen-powered CO fixation.
Authors: Helge M Dietrich / Ricardo D Righetto / Anuj Kumar / Wojciech Wietrzynski / Raphael Trischler / Sandra K Schuller / Jonathan Wagner / Fabian M Schwarz / Benjamin D Engel / Volker Müller / Jan M Schuller /
Abstract: Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO ...Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO fixation-hydrogen-dependent CO reductase (HDCR)-which directly converts H and CO into formic acid. HDCR reduces CO with a higher activity than any other known biological or chemical catalyst, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.
History
DepositionJan 19, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14169.png

Downloads & links

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Map

FileDownload / File: emd_14169.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.4 Angstrom Cryo-EM structure of HDCR complex. The data was processed using cryosparc software.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 352 pix.
= 383.68 Å		1.09 Å/pix.
x 352 pix.
= 383.68 Å		1.09 Å/pix.
x 352 pix.
= 383.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.7795685 - 2.3978634
Average (Standard dev.)0.0014431245 (±0.02906653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 383.68002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Hydrogen-dependent CO2 reductase (HDCR) complex with iron-sulphur...

EntireName: Hydrogen-dependent CO2 reductase (HDCR) complex with iron-sulphur clusters and the H-cluster.
Components
  • Complex: Hydrogen-dependent CO2 reductase (HDCR) complex with iron-sulphur clusters and the H-cluster.
    • Protein or peptide: Hydrogen dependent carbon dioxide reductase subunit HycB3
    • Protein or peptide: Hydrogen dependent carbon dioxide reductase subunit HycB4
    • Protein or peptide: Hydrogen dependent carbon dioxide reductase subunit HydA2
    • Protein or peptide: Hydrogen dependent carbon dioxide reductase subunit FdhF
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)

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Supramolecule #1: Hydrogen-dependent CO2 reductase (HDCR) complex with iron-sulphur...

SupramoleculeName: Hydrogen-dependent CO2 reductase (HDCR) complex with iron-sulphur clusters and the H-cluster.
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: A single functional unit of HDCR complex consists of 4 subunits - FdhF, HydA2, HycB3, and HycB4(1)
Source (natural)Organism: Thermoanaerobacter kivui LKT-1 (bacteria)

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Macromolecule #1: Hydrogen dependent carbon dioxide reductase subunit HycB3

MacromoleculeName: Hydrogen dependent carbon dioxide reductase subunit HycB3
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Oxidoreductases
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)
Molecular weightTheoretical: 20.520934 KDa
SequenceString:
MPNRFVIADP KRCLGCYTCI AACAFVHEEQ GLQPFPRLYL TYTSEGIMPI QCRHCEDAPC AEVCPVEAIK KEGNAIIIDE KACIGCKTC LLACSFGAID FSVQDSLEQS IFKDIKENLM QDQKTQQRIV AVKCDLCNFR EEGPACVQFC PTKALKLVDG D EINKMVKN KRTVNVESLL SVYGTK

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Macromolecule #2: Hydrogen dependent carbon dioxide reductase subunit HycB4

MacromoleculeName: Hydrogen dependent carbon dioxide reductase subunit HycB4
type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: Oxidoreductases
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)
Molecular weightTheoretical: 23.05218 KDa
SequenceString: MYQKVNCYSI LFLKGVDKMK TQLNPFVVAN PAKCIGCKAC EVACFAVHNR NNHVGATVGT VSIPVIPRLH LIKTEHGTMP IQCRHCEDA PCANVCTVGA IKREGNAIVV DEKLCIGCKS CLLACPFGAI ELLPQYEDGR EVFQINLKEE SESGLVQEPR I IAYKCDLC ...String:
MYQKVNCYSI LFLKGVDKMK TQLNPFVVAN PAKCIGCKAC EVACFAVHNR NNHVGATVGT VSIPVIPRLH LIKTEHGTMP IQCRHCEDA PCANVCTVGA IKREGNAIVV DEKLCIGCKS CLLACPFGAI ELLPQYEDGR EVFQINLKEE SESGLVQEPR I IAYKCDLC NDLGEPACVK ACPENALTLV MPTEMKKARN KEAALSFLRV VR

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Macromolecule #3: Hydrogen dependent carbon dioxide reductase subunit HydA2

MacromoleculeName: Hydrogen dependent carbon dioxide reductase subunit HydA2
type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO / EC number: ferredoxin hydrogenase
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)
Molecular weightTheoretical: 51.43027 KDa
SequenceString: MSANKAIINI DQELCTGCRR CAEVCPVDAI EGEKGKPQKI NTEVCVMCGQ CVQKCSSYAS YFDESITPRN VKLQERGMLD SVKEPLFAA YNLGYARQVK EALENPQLFK VVQCAPAIRV SIAEEFGLDL GDLTPGKLVA ALRRLNFDRV YDTNFGADLT I IEEANELV ...String:
MSANKAIINI DQELCTGCRR CAEVCPVDAI EGEKGKPQKI NTEVCVMCGQ CVQKCSSYAS YFDESITPRN VKLQERGMLD SVKEPLFAA YNLGYARQVK EALENPQLFK VVQCAPAIRV SIAEEFGLDL GDLTPGKLVA ALRRLNFDRV YDTNFGADLT I IEEANELV KRIKEGKDLP MFTSCCPAWV KFAEQTYPEL LKHISTCKSP QQMTGAIIKT YGAKINNVDP AKIFSVSVMP CT CKSYESD RPEMRSSGYK DVDLVITTRE LAHLMKDKGI DFATLPDEEF DSPLGNYTGA ATIFGNTGGV MEAALRTAYE LIT KKPIPN IDIEFVRGGE GIRTATVQVG ELELKIAVVS GLKNVIPILE DIKKNKCDLH FVEVMTCPEG CISGGGQPKL LLEE YREVA YKKRKEALYK HDAELELRKS HENPAIKKLY EEFLGEPLGK QSHHLLHTKY TPRKKV

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Macromolecule #4: Hydrogen dependent carbon dioxide reductase subunit FdhF

MacromoleculeName: Hydrogen dependent carbon dioxide reductase subunit FdhF
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: formate dehydrogenase
Source (natural)Organism: Thermoanaerobacter kivui (bacteria)
Molecular weightTheoretical: 82.505711 KDa
SequenceString: MKDGKQEKVL TTCPYCGTGC GLYLKVENEK IVGVEPDKLH PVNQGELCIK GYYGYKYVHD PRRLTSPLIK KNGKFVPVSW DEALNFIAN GLKKIKSEYG SDAFAMFCSA RATNEDNYAA QKFARAVIGI NNVDHCARLC HAPTVAGLAM TLGSGAMTNS I PEISTYSD ...String:
MKDGKQEKVL TTCPYCGTGC GLYLKVENEK IVGVEPDKLH PVNQGELCIK GYYGYKYVHD PRRLTSPLIK KNGKFVPVSW DEALNFIAN GLKKIKSEYG SDAFAMFCSA RATNEDNYAA QKFARAVIGI NNVDHCARLC HAPTVAGLAM TLGSGAMTNS I PEISTYSD VIFIIGSNTA ECHPLIAAHV IKAKERGAKL IVADPRMNAM VHKADIWLRV PSGYNIPLIN GMIHIIIKEG LV KTDFVKN HAVGFEEMAK AVEKYTPEYV EELTGIPKKD LIKAARFYGQ AQAAAILYSM GVTQFSHGTG NVVSLANLAV ITG NLGRPG AGICPLRGQN NVQGACDVGA LPNVLPGYLD VTKEQNRERF EKVWGVKLPS NIGLRVTEVP DAILNKRVRA LYIF GENPI MSDPDSDHLR HALEHLDLLI VQDIFLTETA RLAHVVLPAA CWAEKDGTFT NTERRVQRVR KAVEAPGEAK PDWWI FSQI AERMGYTGMQ YNNVQEIWDE VRKIVPEKFG GISYARLEKE KGLAWPCPTE DHTGTPILYL GGKFATPSGK AQMYPV IFY PNTCICDEGA EKQDFNHVIV GSIAELPDEE YPFTLTTGRR VYHYHTATMT RKSPVIDQIA PQELVEINPQ DATRLGI ND GDFLRVSTRR GYVATRAWVT ERVPKGTIFM TFHYWEACCN ELTNTASDAI CCIPEFKVAA AKVEKISQVE AQAILKEK I EKYQVELEKD VANMLAKEKG GK

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 52 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

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Macromolecule #6: dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kap...

MacromoleculeName: dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
type: ligand / ID: 6 / Number of copies: 6 / Formula: 402
Molecular weightTheoretical: 354.953 Da
Chemical component information

ChemComp-402:
dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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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: 5.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 719937

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