8A5E

Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state


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

Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC.

Katsyv, A.Kumar, A.Saura, P.Poverlein, M.C.Freibert, S.A.T Stripp, S.Jain, S.Gamiz-Hernandez, A.P.Kaila, V.R.I.Muller, V.Schuller, J.M.

(2023) J Am Chem Soc 145: 5696-5709

  • DOI: https://doi.org/10.1021/jacs.2c11683
  • Primary Citation of Related Structures:  
    7Q4V, 7Q4W, 8A5E, 8A6T, 8BEW

  • PubMed Abstract: 

    Electron bifurcation is a fundamental energy coupling mechanism widespread in microorganisms that thrive under anoxic conditions. These organisms employ hydrogen to reduce CO 2 , but the molecular mechanisms have remained enigmatic. The key enzyme responsible for powering these thermodynamically challenging reactions is the electron-bifurcating [FeFe]-hydrogenase HydABC that reduces low-potential ferredoxins (Fd) by oxidizing hydrogen gas (H 2 ). By combining single-particle cryo-electron microscopy (cryoEM) under catalytic turnover conditions with site-directed mutagenesis experiments, functional studies, infrared spectroscopy, and molecular simulations, we show that HydABC from the acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui employ a single flavin mononucleotide (FMN) cofactor to establish electron transfer pathways to the NAD(P) + and Fd reduction sites by a mechanism that is fundamentally different from classical flavin-based electron bifurcation enzymes. By modulation of the NAD(P) + binding affinity via reduction of a nearby iron-sulfur cluster, HydABC switches between the exergonic NAD(P) + reduction and endergonic Fd reduction modes. Our combined findings suggest that the conformational dynamics establish a redox-driven kinetic gate that prevents the backflow of the electrons from the Fd reduction branch toward the FMN site, providing a basis for understanding general mechanistic principles of electron-bifurcating hydrogenases.


  • Organizational Affiliation

    Institut für Zytobiologie im Zentrum SYNMIKRO, Philipps-University of Marburg, Marburg 35032, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iron hydrogenase HydA1
A, D
583Acetobacterium woodii DSM 1030Mutation(s): 0 
EC: 1.12.7.2
UniProt
Find proteins for H6LFG3 (Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1))
Explore H6LFG3 
Go to UniProtKB:  H6LFG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6LFG3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Iron hydrogenase HydB599Acetobacterium woodii DSM 1030Mutation(s): 0 
EC: 1.12.7.2
UniProt
Find proteins for H6LFG4 (Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1))
Explore H6LFG4 
Go to UniProtKB:  H6LFG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6LFG4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Iron hydrogenase HydC156Acetobacterium woodii DSM 1030Mutation(s): 0 
EC: 1.12.7.2
UniProt
Find proteins for H6LFG7 (Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1))
Explore H6LFG7 
Go to UniProtKB:  H6LFG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6LFG7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
P [auth B]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
N [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
HC1 (Subject of Investigation/LOI)
Query on HC1

Download Ideal Coordinates CCD File 
J [auth A],
W [auth D]
2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER
C5 H8 Fe2 O7 S2
DXKOXSKJHMBSFW-UHFFFAOYSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth A]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth A],
L [auth B],
M [auth B],
O [auth B],
R [auth D],
S [auth D],
T [auth D],
V [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth C],
U [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
K [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

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 Union715311 (VRIK)
European Research Council (ERC)European Union741791
Knut and Alice Wallenberg FoundationSwedenVRIK
German Research Foundation (DFG)GermanySFB1078
Swedish Research CouncilSweden016-07213

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references
  • Version 1.2: 2023-03-29
    Changes: Database references