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- PDB-7t2r: Structure of electron bifurcating Ni-Fe hydrogenase complex HydAB... -

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Entry
Database: PDB / ID: 7t2r
TitleStructure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state
Components(NiFe hydrogenase ...) x 5
KeywordsOXIDOREDUCTASE / hydrogenase complex / electron bifurcation
Function / homology
Function and homology information


ferredoxin hydrogenase activity / iron-sulfur cluster binding / nickel cation binding / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / membrane / metal ion binding
Similarity search - Function
Nickel-dependent hydrogenases large subunit signature 2. / Molybdopterin oxidoreductase Fe4S4 domain / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Soluble ligand binding domain ...Nickel-dependent hydrogenases large subunit signature 2. / Molybdopterin oxidoreductase Fe4S4 domain / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / 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. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
NICKEL (III) ION / CARBONMONOXIDE-(DICYANO) IRON / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Coenzyme F420-reducing hydrogenase, alpha subunit / Coenzyme F420-reducing hydrogenase, gamma subunit / Putative anaerobic dehydrogenase / NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit / NADH-quinone oxidoreductase, E subunit
Similarity search - Component
Biological speciesAcetomicrobium mobile (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFeng, X. / Li, H.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure and electron transfer pathways of an electron-bifurcating NiFe-hydrogenase.
Authors: Xiang Feng / Gerrit J Schut / Dominik K Haja / Michael W W Adams / Huilin Li /
Abstract: Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents ...Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents the fourth group, but its bifurcation site is unknown. We report cryo-EM structures of the related NiFe-HydABCSL hydrogenase that reversibly oxidizes H and couples endergonic reduction of ferredoxin with exergonic reduction of NAD. FMN surrounded by a unique arrangement of iron sulfur clusters forms the bifurcating center. NAD binds to FMN in HydB, and electrons from H via HydA to a HydB [4Fe-4S] cluster enable the FMN to reduce NAD. Low-potential electron transfer from FMN to the HydC [2Fe-2S] cluster and subsequent reduction of a uniquely penta-coordinated HydB [2Fe-2S] cluster require conformational changes, leading to ferredoxin binding and reduction by a [4Fe-4S] cluster in HydB. This work clarifies the electron transfer pathways for a large group of hydrogenases underlying many essential functions in anaerobic microorganisms.
History
DepositionDec 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: NiFe hydrogenase subunit A
B: NiFe hydrogenase subunit B
C: NiFe hydrogenase subunit C
D: NiFe hydrogenase large subunit
E: NiFe hydrogenase small subunit
F: NiFe hydrogenase subunit A
G: NiFe hydrogenase subunit B
H: NiFe hydrogenase subunit C
I: NiFe hydrogenase large subunit
J: NiFe hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,86132
Polymers466,19710
Non-polymers5,66422
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NiFe hydrogenase ... , 5 types, 10 molecules AFBGCHDIEJ

#1: Protein NiFe hydrogenase subunit A / / Anaerobic dehydrogenase


Mass: 76799.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BYB4
#2: Protein NiFe hydrogenase subunit B / / NADH:ubiquinone oxidoreductase / NADH-binding (51 kD) subunit


Mass: 65557.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BYB5
#3: Protein NiFe hydrogenase subunit C / / NADH-quinone oxidoreductase / E subunit


Mass: 17482.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BYB8
#4: Protein NiFe hydrogenase large subunit / / Coenzyme F420-reducing hydrogenase / alpha subunit


Mass: 53294.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BYB2
#5: Protein NiFe hydrogenase small subunit / / Coenzyme F420-reducing hydrogenase / gamma subunit


Mass: 19965.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acetomicrobium mobile (bacteria) / References: UniProt: I4BYB3

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Non-polymers , 4 types, 22 molecules

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


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-3NI / NICKEL (III) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O / 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: NiFe hydrogenase complex ABCSL / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 0.5 MDa / Experimental value: YES
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2300 mMSodium chlorideNaclSodium chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: -2000 nm / Nominal defocus min: -1000 nm
Image recordingElectron dose: 76 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
9cryoSPARC3.2initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 269151 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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