8RJA | pdb_00008rja

Crystal structure of the F420-reducing formylmethanofuran dehydrogenase complex from the ethanotroph Candidatus Ethanoperedens thermophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.210 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Ethane-oxidising archaea couple CO 2 generation to F 420 reduction.

Lemaire, O.N.Wegener, G.Wagner, T.

(2024) Nat Commun 15: 9065-9065

  • DOI: https://doi.org/10.1038/s41467-024-53338-7
  • Primary Citation Related Structures: 
    8RIU, 8RJA

  • PubMed Abstract: 

    The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO 2 -forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO 2 -generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F 420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F 420 reductase. Accordingly, both systems exhibit robust coupled F 420 -reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F 420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F 420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy.


  • Organizational Affiliation
    • Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.

Macromolecule Content 

  • Total Structure Weight: 412.54 kDa 
  • Atom Count: 30,528 
  • Modeled Residue Count: 3,602 
  • Deposited Residue Count: 3,640 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase subunit A
A, G
567Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
EC: 3.5.2.5
UniProt
Find proteins for A0ACD6B9F9 (Candidatus Methanoperedenaceae archaeon GB50)
Explore A0ACD6B9F9 
Go to UniProtKB:  A0ACD6B9F9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9F9
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase subunit B
B, H
430Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
UniProt
Find proteins for A0ACD6B9F8 (Candidatus Methanoperedenaceae archaeon GB50)
Explore A0ACD6B9F8 
Go to UniProtKB:  A0ACD6B9F8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9F8
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
formylmethanofuran dehydrogenase
C, I
253Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
EC: 1.2.7.12
UniProt
Find proteins for A0ACD6B9G0 (Candidatus Methanoperedenaceae archaeon GB50)
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Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9G0
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Formylmethanofuran dehydrogenase subunit D
D, J
126Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
EC: 1.2.7.12
UniProt
Find proteins for A0ACD6B9F7 (Candidatus Methanoperedenaceae archaeon GB50)
Explore A0ACD6B9F7 
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Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9F7
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
E, K
359Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
UniProt
Find proteins for A0A7R9N9K9 (Candidatus Methanoperedenaceae archaeon GB50)
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Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9N9K9
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
F, L
85Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
EC: 1.6.5.11
UniProt
Find proteins for A0A7R9MZV2 (Candidatus Methanoperedenaceae archaeon GB50)
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Entity Groups
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UniProt GroupA0A7R9MZV2
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Reference Sequence

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
JA [auth E],
TB [auth K]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MGD
(Subject of Investigation/LOI)

Query on MGD



Download:Ideal Coordinates CCD File
AA [auth B],
BA [auth B],
DB [auth H],
EB [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
PE4

Query on PE4



Download:Ideal Coordinates CCD File
EA [auth B],
PB [auth I],
R [auth A]
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
BB [auth H]
HA [auth E]
IA [auth E]
KA [auth E]
RA [auth F]
BB [auth H],
HA [auth E],
IA [auth E],
KA [auth E],
RA [auth F],
RB [auth K],
SA [auth F],
SB [auth K],
UB [auth K],
Y [auth B],
YB [auth L],
ZB [auth L]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
NB [auth I]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
W
(Subject of Investigation/LOI)

Query on W



Download:Ideal Coordinates CCD File
CB [auth H],
Z [auth B]
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
O [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
FB [auth H]
IB [auth H]
JB [auth H]
LA [auth E]
MB [auth I]
FB [auth H],
IB [auth H],
JB [auth H],
LA [auth E],
MB [auth I],
OB [auth I],
P [auth A],
T [auth A],
W [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
UA [auth G],
VA [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AB [auth G]
FA [auth B]
KB [auth H]
MA [auth E]
NA [auth E]
AB [auth G],
FA [auth B],
KB [auth H],
MA [auth E],
NA [auth E],
OA [auth E],
PA [auth E],
U [auth A],
V [auth A],
VB [auth K],
WB [auth K],
XA [auth G],
YA [auth G],
ZA [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
DA [auth B],
HB [auth H],
Q [auth A],
QB [auth I],
S [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
AC [auth L],
GA [auth C],
TA [auth F],
X [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
H2S
(Subject of Investigation/LOI)

Query on H2S



Download:Ideal Coordinates CCD File
CA [auth B],
GB [auth H]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
LB [auth H],
QA [auth E],
WA [auth G],
XB [auth K]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, G
L-PEPTIDE LINKINGC7 H14 N2 O4LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.627α = 90
b = 135.636β = 90.49
c = 149.902γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyWA 4053/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references, Structure summary