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- PDB-7bkd: Formate dehydrogenase - heterodisulfide reductase - formylmethano... -

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Basic information

Entry
Database: PDB / ID: 7bkd
TitleFormate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodislfide reductase core and mobile arm in conformational state 1, composite structure)
Components
  • (CoB--CoM heterodisulfide reductase subunit ...CoB—CoM heterodisulfide reductase) x 2
  • CoB--CoM heterodisulfide reductase iron-sulfur subunit A
  • F420-non-reducing hydrogenase subunit D
  • Formate dehydrogenase, beta subunit (F420)
  • Formate dehydrogenase
KeywordsOXIDOREDUCTASE / methanogenesis / flavin-based electron bifurcation / CO2-fixation / formate dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / formate metabolic process / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / FAD dependent oxidoreductase / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal ...F420-non-reducing hydrogenase iron-sulfur subunit D / Cysteine-rich domain / CoB--CoM heterodisulphide reductase, subunit B / CoB--CoM heterodisulphide reductase, subunit C / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / Methyl-viologen-reducing hydrogenase, delta subunit / Cysteine-rich domain / FAD dependent oxidoreductase / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / 4Fe-4S dicluster domain / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-helical ferredoxin / Molybdopterin oxidoreductase Fe4S4 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 dicluster domain / 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
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / F420-non-reducing hydrogenase subunit D / CoB--CoM heterodisulfide reductase iron-sulfur subunit A / CoB--CoM heterodisulfide reductase subunit B / CoB--CoM heterodisulfide reductase subunit C / Formate dehydrogenase, beta subunit (F420) / Formate dehydrogenase, alpha subunit (F420)
Similarity search - Component
Biological speciesMethanospirillum hungatei JF-1 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsPfeil-Gardiner, O. / Watanabe, T. / Shima, S. / Murphy, B.J.
Funding support Germany, Japan, 4items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SH 87/1-1 Germany
Japan Society for the Promotion of Science (JSPS) Japan
Alexander von Humboldt Foundation Germany
CitationJournal: Science / Year: 2021
Title: Three-megadalton complex of methanogenic electron-bifurcating and CO-fixing enzymes.
Authors: Tomohiro Watanabe / Olivia Pfeil-Gardiner / Jörg Kahnt / Jürgen Koch / Seigo Shima / Bonnie J Murphy /
Abstract: The first reaction of the methanogenic pathway from carbon dioxide (CO) is the reduction and condensation of CO to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly ...The first reaction of the methanogenic pathway from carbon dioxide (CO) is the reduction and condensation of CO to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd). Strongly reducing electrons for this reaction are generated by heterodisulfide reductase (Hdr) in complex with hydrogenase or formate dehydrogenase (Fdh) using a flavin-based electron-bifurcation mechanism. Here, we report enzymological and structural characterizations of Fdh-Hdr-Fmd complexes from . The complexes catalyze this reaction using electrons from formate and the reduced form of the electron carrier F. Conformational changes in HdrA mediate electron bifurcation, and polyferredoxin FmdF directly transfers electrons to the CO reduction site, as evidenced by methanofuran-dependent flavin-based electron bifurcation even without free ferredoxin, a diffusible electron carrier between Hdr and Fmd. Conservation of Hdr and Fmd structures suggests that this complex is common among hydrogenotrophic methanogens.
History
DepositionJan 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
C: CoB--CoM heterodisulfide reductase subunit C
B: CoB--CoM heterodisulfide reductase subunit B
a: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
c: CoB--CoM heterodisulfide reductase subunit C
b: CoB--CoM heterodisulfide reductase subunit B
F: F420-non-reducing hydrogenase subunit D
E: Formate dehydrogenase, beta subunit (F420)
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)402,55835
Polymers392,2909
Non-polymers10,26926
Water0
1


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

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Components

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Protein , 4 types, 5 molecules AaFED

#1: Protein CoB--CoM heterodisulfide reductase iron-sulfur subunit A


Mass: 72885.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea)
References: UniProt: Q2FKZ1, Oxidoreductases; Acting on a sulfur group of donors
#4: Protein F420-non-reducing hydrogenase subunit D


Mass: 15692.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FKZ0
#5: Protein Formate dehydrogenase, beta subunit (F420) /


Mass: 45639.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea)
References: UniProt: Q2FME3, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors
#6: Protein Formate dehydrogenase /


Mass: 75911.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FRK1, formate dehydrogenase

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CoB--CoM heterodisulfide reductase subunit ... , 2 types, 4 molecules CcBb

#2: Protein CoB--CoM heterodisulfide reductase subunit C / CoB—CoM heterodisulfide reductase


Mass: 21706.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FKZ3
#3: Protein CoB--CoM heterodisulfide reductase subunit B / CoB—CoM heterodisulfide reductase


Mass: 32930.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FKZ2

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Non-polymers , 4 types, 26 molecules

#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#9: Chemical
ChemComp-9S8 / Non-cubane [4Fe-4S]-cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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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: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 0.948 MDa / Experimental value: NO
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea) / Cellular location: cytoplasm
Buffer solutionpH: 7.6
Buffer componentConc.: 25 mM / Name: Tris-HClTris / Formula: Tris-HClTris
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Preparation in an anaerobic tent (O2 < 20 ppm at all times, nearly always < 2ppm)
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 293 K

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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 / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 8745
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

Software
NameVersionClassificationNB
PHENIX(1.18.2_3874:phenix.real_space_refine)refinement
PDB_EXTRACT3.27data extraction
EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
5RELION3.1CTF correction
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
Image processingDetails: Recorded in counted mode
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277450
Details: This applies to the map of the mobile arm in state1. The uploaded map is a composite map.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 62.27 Å2 / Biso mean: 31.7842 Å2 / Biso min: 5.51 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00525401
ELECTRON MICROSCOPYf_angle_d0.69134536
ELECTRON MICROSCOPYf_chiral_restr0.0493827
ELECTRON MICROSCOPYf_plane_restr0.0044393
ELECTRON MICROSCOPYf_dihedral_angle_d11.7973426

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