7BKD

Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodislfide reductase core and mobile arm in conformational state 1, composite structure)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Three-megadalton complex of methanogenic electron-bifurcating and CO 2 -fixing enzymes.

Watanabe, T.Pfeil-Gardiner, O.Kahnt, J.Koch, J.Shima, S.Murphy, B.J.

(2021) Science 373: 1151-1156

  • DOI: https://doi.org/10.1126/science.abg5550
  • Primary Citation of Related Structures:  
    7BKB, 7BKC, 7BKD, 7BKE

  • PubMed Abstract: 

    The first reaction of the methanogenic pathway from carbon dioxide (CO 2 ) is the reduction and condensation of CO 2 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 Methanospirillum hungatei . The complexes catalyze this reaction using electrons from formate and the reduced form of the electron carrier F 420 . Conformational changes in HdrA mediate electron bifurcation, and polyferredoxin FmdF directly transfers electrons to the CO 2 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.


  • Organizational Affiliation

    Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CoB--CoM heterodisulfide reductase iron-sulfur subunit AA,
D [auth a]
671Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.8
UniProt
Find proteins for Q2FKZ1 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
Explore Q2FKZ1 
Go to UniProtKB:  Q2FKZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FKZ1
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CoB--CoM heterodisulfide reductase subunit CB [auth C],
E [auth c]
191Methanospirillum hungatei JF-1Mutation(s): 0 
UniProt
Find proteins for Q2FKZ3 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Go to UniProtKB:  Q2FKZ3
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UniProt GroupQ2FKZ3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CoB--CoM heterodisulfide reductase subunit BC [auth B],
F [auth b]
296Methanospirillum hungatei JF-1Mutation(s): 0 
UniProt
Find proteins for Q2FKZ2 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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UniProt GroupQ2FKZ2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
F420-non-reducing hydrogenase subunit DG [auth F]140Methanospirillum hungatei JF-1Mutation(s): 0 
UniProt
Find proteins for Q2FKZ0 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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UniProt GroupQ2FKZ0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, beta subunit (F420)H [auth E]414Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99
UniProt
Find proteins for Q2FME3 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenaseI [auth D]686Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.17.1.9 (PDB Primary Data), 1.2.99 (UniProt)
UniProt
Find proteins for Q2FRK1 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Go to UniProtKB:  Q2FRK1
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UniProt GroupQ2FRK1
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
HA [auth E],
K [auth A],
V [auth a]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
9S8 (Subject of Investigation/LOI)
Query on 9S8

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AA [auth b],
BA [auth b],
S [auth B],
T [auth B]
Non-cubane [4Fe-4S]-cluster
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SF4
Query on SF4

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DA [auth E]
EA [auth E]
FA [auth E]
GA [auth E]
IA [auth D]
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth E],
IA [auth D],
J [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth C],
R [auth C],
U [auth a],
W [auth a],
X [auth a],
Y [auth c],
Z [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
CA [auth F]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanySH 87/1-1
Japan Society for the Promotion of Science (JSPS)Japan--
Alexander von Humboldt FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary