7BKC

Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (dimeric, 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


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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,
N [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))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
F420-non-reducing hydrogenase subunit DB [auth F],
O [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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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, beta subunit (F420)C [auth E],
P [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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CoB--CoM heterodisulfide reductase subunit CD [auth C],
Q [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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CoB--CoM heterodisulfide reductase subunit BE [auth B],
R [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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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenaseF [auth D],
S [auth d]
686Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.17.1.9
UniProt
Find proteins for Q2FRK1 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenaseG [auth I],
T [auth i]
266Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.7.12
UniProt
Find proteins for Q2FRL8 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit GH [auth L],
U [auth l]
146Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FKZ5 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit AI [auth G],
V [auth g]
571Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FRL9 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit DJ,
W [auth j]
137Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FRF6 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit FK [auth M],
L [auth K],
X [auth m],
Y [auth k]
388Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FKZ4 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase, subunit BM [auth H],
Z [auth h]
443Methanospirillum hungatei JF-1Mutation(s): 0 
EC: 1.2.99.5
UniProt
Find proteins for Q2FRM0 (Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1))
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
BA [auth A],
JB [auth a],
MA [auth E],
UB [auth e]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MGD (Subject of Investigation/LOI)
Query on MGD

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FB [auth H],
GB [auth H],
NC [auth h],
OC [auth h]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
SF4
Query on SF4

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AA [auth A]
AB [auth K]
AC [auth l]
BB [auth K]
BC [auth l]
AA [auth A],
AB [auth K],
AC [auth l],
BB [auth K],
BC [auth l],
CA [auth A],
CB [auth K],
DA [auth A],
DB [auth K],
EA [auth A],
EC [auth m],
FA [auth A],
FC [auth m],
GA [auth A],
GC [auth k],
HB [auth H],
HC [auth k],
IA [auth E],
IB [auth a],
IC [auth k],
JA [auth E],
JC [auth k],
KA [auth E],
KB [auth a],
KC [auth k],
LA [auth E],
LB [auth a],
LC [auth k],
MB [auth a],
NA [auth C],
NB [auth a],
OA [auth C],
OB [auth a],
PC [auth h],
QB [auth e],
RA [auth D],
RB [auth e],
SA [auth L],
SB [auth e],
TA [auth L],
TB [auth e],
VB [auth c],
WA [auth M],
WB [auth c],
XA [auth M],
YA [auth K],
ZA [auth K],
ZB [auth d]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
9S8 (Subject of Investigation/LOI)
Query on 9S8

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PA [auth B],
QA [auth B],
XB [auth b],
YB [auth b]
Non-cubane [4Fe-4S]-cluster
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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HA [auth F],
PB [auth f]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MO
Query on MO

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EB [auth H],
MC [auth h]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
ZN
Query on ZN

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CC [auth g],
DC [auth g],
UA [auth G],
VA [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
I [auth G],
V [auth g]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
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