8RIU | pdb_00008riu

Crystal structure of the F420-reducing carbon monoxide dehydrogenase component from the ethanotroph Candidatus Ethanoperedens thermophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.187 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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: 304.17 kDa 
  • Atom Count: 21,942 
  • Modeled Residue Count: 2,607 
  • Deposited Residue Count: 2,672 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetyl-CoA decarbonylase/synthase complex subunit alpha
A, D
792Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
EC: 1.2.7.4
UniProt
Find proteins for A0A7R9N4A5 (Candidatus Methanoperedenaceae archaeon GB50)
Explore A0A7R9N4A5 
Go to UniProtKB:  A0A7R9N4A5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9N4A5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
B, E
370Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
UniProt
Find proteins for A0A7R9R773 (Candidatus Methanoperedenaceae archaeon GB50)
Explore A0A7R9R773 
Go to UniProtKB:  A0A7R9R773
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9R773
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetyl-CoA decarbonylase/synthase complex subunit epsilon
C, F
174Candidatus Methanoperedentaceae archaeon GB50Mutation(s): 0 
UniProt
Find proteins for A0A7R9N5A2 (Candidatus Methanoperedenaceae archaeon GB50)
Explore A0A7R9N5A2 
Go to UniProtKB:  A0A7R9N5A2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9N5A2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
EA [auth B],
VA [auth E]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
XCC
(Subject of Investigation/LOI)

Query on XCC



Download:Ideal Coordinates CCD File
PA [auth D],
R [auth A]
FE(4)-NI(1)-S(4) CLUSTER
Fe4 Ni S4
QGLWBXDZIHZONR-UHFFFAOYSA-N
PE4

Query on PE4



Download:Ideal Coordinates CCD File
QA [auth D]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
CA [auth B]
DA [auth B]
FA [auth B]
MA [auth D]
NA [auth D]
CA [auth B],
DA [auth B],
FA [auth B],
MA [auth D],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
Q [auth A],
TA [auth E],
UA [auth E],
WA [auth E],
Y [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AB [auth F]
G [auth A]
GA [auth B]
HA [auth C]
IA [auth C]
AB [auth F],
G [auth A],
GA [auth B],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth D],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
XA [auth E],
YA [auth F],
Z [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
BA [auth B]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
BA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
N [auth A],
X [auth A],
ZA [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
AA [auth A],
SA [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
RA [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.187 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.07α = 90
b = 159.213β = 90
c = 191.444γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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