7QV7

Cryo-EM structure of Hydrogen-dependent CO2 reductase.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Membrane-anchored HDCR nanowires drive hydrogen-powered CO 2 fixation.

Dietrich, H.M.Righetto, R.D.Kumar, A.Wietrzynski, W.Trischler, R.Schuller, S.K.Wagner, J.Schwarz, F.M.Engel, B.D.Muller, V.Schuller, J.M.

(2022) Nature 607: 823-830

  • DOI: https://doi.org/10.1038/s41586-022-04971-z
  • Primary Citation of Related Structures:  
    7QV7

  • PubMed Abstract: 

    Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive 1 . Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO 2 fixation-hydrogen-dependent CO 2 reductase (HDCR) 2,3 -which directly converts H 2 and CO 2 into formic acid. HDCR reduces CO 2 with a higher activity than any other known biological or chemical catalyst 4,5 , and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO 2 . However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.


  • Organizational Affiliation

    Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogen dependent carbon dioxide reductase subunit HycB3A,
E [auth G]
184Thermoanaerobacter kivuiMutation(s): 0 
EC: 1
UniProt
Find proteins for A0A097ATJ9 (Thermoanaerobacter kivui)
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Go to UniProtKB:  A0A097ATJ9
Entity Groups  
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UniProt GroupA0A097ATJ9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogen dependent carbon dioxide reductase subunit HycB4210Thermoanaerobacter kivuiMutation(s): 0 
EC: 1
UniProt
Find proteins for A0A097ATK6 (Thermoanaerobacter kivui)
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Go to UniProtKB:  A0A097ATK6
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UniProt GroupA0A097ATK6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogen dependent carbon dioxide reductase subunit HydA2461Thermoanaerobacter kivuiMutation(s): 0 
EC: 1.12.7.2
UniProt
Find proteins for A0A097ATH7 (Thermoanaerobacter kivui)
Explore A0A097ATH7 
Go to UniProtKB:  A0A097ATH7
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UniProt GroupA0A097ATH7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogen dependent carbon dioxide reductase subunit FdhFL [auth S],
O [auth Y]
743Thermoanaerobacter kivuiMutation(s): 0 
EC: 1.2.1.2
UniProt
Find proteins for A0A097ATK5 (Thermoanaerobacter kivui)
Explore A0A097ATK5 
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UniProt GroupA0A097ATK5
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
402 (Subject of Investigation/LOI)
Query on 402

Download Ideal Coordinates CCD File 
DB [auth Q]
EA [auth D]
GB [auth R]
LB [auth V]
QA [auth K]
DB [auth Q],
EA [auth D],
GB [auth R],
LB [auth V],
QA [auth K],
VB [auth Z]
dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
C7 H5 Fe2 N3 O3 S2
LJPDYWPSPOWMIB-UHFFFAOYSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth Q]
BA [auth C]
BB [auth Q]
CA [auth D]
AA [auth C],
AB [auth Q],
BA [auth C],
BB [auth Q],
CA [auth D],
CB [auth Q],
DA [auth D],
EB [auth R],
FA [auth D],
FB [auth R],
GA [auth G],
HA [auth G],
HB [auth R],
IA [auth G],
IB [auth S],
JA [auth G],
JB [auth V],
KA [auth J],
KB [auth V],
LA [auth J],
MA [auth J],
MB [auth V],
NA [auth J],
NB [auth X],
OA [auth K],
OB [auth X],
PA [auth K],
PB [auth X],
Q [auth A],
QB [auth X],
R [auth A],
RA [auth K],
RB [auth Y],
S [auth A],
SA [auth N],
SB [auth Z],
T [auth A],
TA [auth N],
TB [auth Z],
U [auth B],
UA [auth N],
UB [auth Z],
V [auth B],
VA [auth N],
W [auth B],
WA [auth P],
X [auth B],
XA [auth P],
Y [auth C],
YA [auth P],
Z [auth C],
ZA [auth P]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySCHU 3364/1-1
European Research Council (ERC)European Union741791
German Research Foundation (DFG)GermanyFOR 2092
Alexander von Humboldt FoundationGermany--
German Research Foundation (DFG)Germany20016/446

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2022-08-10
    Changes: Database references