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

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Entry
Database: PDB / ID: 7bkc
TitleFormate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (dimeric, composite structure)
Components
  • (CoB--CoM heterodisulfide reductase subunit ...) x 2
  • (Formylmethanofuran dehydrogenase, subunit ...) x 5
  • CoB--CoM heterodisulfide reductase iron-sulfur subunit A
  • F420-non-reducing hydrogenase subunit D
  • Formate dehydrogenase
  • Formate dehydrogenase, beta subunit (F420)
  • Formylmethanofuran dehydrogenase
KeywordsOXIDOREDUCTASE / methanogenesis / flavin-based electron bifurcation / CO2-fixation / formate dehydrogenase
Function / homology
Function and homology information


formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate metabolic process / methanogenesis, from carbon dioxide / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis ...formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With unknown physiological acceptors / CoB--CoM heterodisulfide reductase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / formate metabolic process / methanogenesis, from carbon dioxide / Oxidoreductases; Acting on a sulfur group of donors / methanogenesis / formate dehydrogenase (NAD+) activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdopterin cofactor binding / NADH dehydrogenase activity / iron-sulfur cluster binding / transition metal ion binding / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / membrane / plasma membrane
Similarity search - Function
Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit B / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / : / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily ...Polyferredoxin MvhB-like / : / Formylmethanofuran dehydrogenase, subunit B / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #140 / : / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / FAD dependent oxidoreductase / F420-non-reducing hydrogenase iron-sulfur subunit D / Methyl-viologen-reducing hydrogenase, delta subunit / CoB--CoM heterodisulphide reductase, subunit C / CoB--CoM heterodisulphide reductase, subunit B / : / H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like / : / Cysteine-rich domain / Cysteine-rich domain / Amidohydrolase 3 / Amidohydrolase family / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / 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 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Prokaryotic molybdopterin oxidoreductases signature 2. / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / 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 / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Metal-dependent hydrolase, composite domain superfamily / : / Aspartate decarboxylase-like domain superfamily / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Metal-dependent hydrolase / 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 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / MOLYBDENUM ATOM / 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 ...Non-cubane [4Fe-4S]-cluster / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / MOLYBDENUM ATOM / 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 / Formylmethanofuran dehydrogenase, subunit F / Formylmethanofuran dehydrogenase, subunit G / Formate dehydrogenase, beta subunit (F420) / Formylmethanofuran dehydrogenase, subunit D / Formate dehydrogenase, alpha subunit (F420) / formylmethanofuran dehydrogenase / Formylmethanofuran dehydrogenase, subunit A / formylmethanofuran dehydrogenase subunit B
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
Citation
Journal: 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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Structure visualization

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Assembly

Deposited unit
A: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
F: F420-non-reducing hydrogenase subunit D
E: Formate dehydrogenase, beta subunit (F420)
C: CoB--CoM heterodisulfide reductase subunit C
B: CoB--CoM heterodisulfide reductase subunit B
D: Formate dehydrogenase
I: Formylmethanofuran dehydrogenase
L: Formylmethanofuran dehydrogenase, subunit G
G: Formylmethanofuran dehydrogenase, subunit A
J: Formylmethanofuran dehydrogenase, subunit D
M: Formylmethanofuran dehydrogenase, subunit F
K: Formylmethanofuran dehydrogenase, subunit F
H: Formylmethanofuran dehydrogenase, subunit B
a: CoB--CoM heterodisulfide reductase iron-sulfur subunit A
f: F420-non-reducing hydrogenase subunit D
e: Formate dehydrogenase, beta subunit (F420)
c: CoB--CoM heterodisulfide reductase subunit C
b: CoB--CoM heterodisulfide reductase subunit B
d: Formate dehydrogenase
i: Formylmethanofuran dehydrogenase
l: Formylmethanofuran dehydrogenase, subunit G
g: Formylmethanofuran dehydrogenase, subunit A
j: Formylmethanofuran dehydrogenase, subunit D
m: Formylmethanofuran dehydrogenase, subunit F
k: Formylmethanofuran dehydrogenase, subunit F
h: Formylmethanofuran dehydrogenase, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,070,09694
Polymers1,044,90126
Non-polymers25,19568
Water00
1


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

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Components

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Protein , 5 types, 10 molecules AaFfEeDdIi

#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
#2: Protein F420-non-reducing hydrogenase subunit D


Mass: 15692.425 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FKZ0
#3: Protein Formate dehydrogenase, beta subunit (F420)


Mass: 45639.895 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea) / References: UniProt: Q2FRK1, formate dehydrogenase
#7: Protein Formylmethanofuran dehydrogenase


Mass: 28696.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea)
References: UniProt: Q2FRL8, formylmethanofuran dehydrogenase

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

#4: Protein CoB--CoM heterodisulfide reductase subunit C


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
#5: Protein CoB--CoM heterodisulfide reductase subunit B


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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Formylmethanofuran dehydrogenase, subunit ... , 5 types, 12 molecules LlGgJjMKmkHh

#8: Protein Formylmethanofuran dehydrogenase, subunit G


Mass: 16388.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea)
References: UniProt: Q2FKZ5, formylmethanofuran dehydrogenase
#9: Protein Formylmethanofuran dehydrogenase, subunit A


Mass: 63636.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea)
References: UniProt: Q2FRL9, formylmethanofuran dehydrogenase
#10: Protein Formylmethanofuran dehydrogenase, subunit D


Mass: 15157.499 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea)
References: UniProt: Q2FRF6, formylmethanofuran dehydrogenase
#11: Protein
Formylmethanofuran dehydrogenase, subunit F


Mass: 42216.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea)
References: UniProt: Q2FKZ4, formylmethanofuran dehydrogenase
#12: Protein Formylmethanofuran dehydrogenase, subunit B


Mass: 49371.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanospirillum hungatei JF-1 (archaea)
References: UniProt: Q2FRM0, formylmethanofuran dehydrogenase

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Non-polymers , 7 types, 68 molecules

#13: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Fe4S4
#14: 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
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#16: 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
#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#18: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#19: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / 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: Dimeric formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex
Type: COMPLEX / Entity ID: #1-#12 / 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-HCl / Formula: Tris-HCl
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)
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
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 FIELD / 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

SoftwareName: PHENIX / Classification: refinement
EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
5RELION3.1CTF correction
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
14RELION3.13D reconstruction
Image processingDetails: Recorded in counted mode
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1239454
Details: As this is a composite map, the resolution is estimated from the resolutions for masked refinements of several regions, which range from 2.6 to 3.7 A.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 96.67 Å2 / Biso mean: 46.8325 Å2 / Biso min: 6.51 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008565654
ELECTRON MICROSCOPYf_angle_d0.827889250
ELECTRON MICROSCOPYf_chiral_restr0.0579916
ELECTRON MICROSCOPYf_plane_restr0.005611362
ELECTRON MICROSCOPYf_dihedral_angle_d11.59528828

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