9F47 | pdb_00009f47

crystal structure of [FeFe]-hydrogenase CbA5H from Clostridium beijerinckii in Hinact state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.298 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Model: experimental
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Literature

Structural determinants of oxygen resistance and Zn 2+ -mediated stability of the [FeFe]-hydrogenase from Clostridium beijerinckii.

Duan, J.Rutz, A.Kawamoto, A.Naskar, S.Edenharter, K.Leimkuhler, S.Hofmann, E.Happe, T.Kurisu, G.

(2025) Proc Natl Acad Sci U S A 122: e2416233122-e2416233122

  • DOI: https://doi.org/10.1073/pnas.2416233122
  • Primary Citation of Related Structures:  
    8ZQD, 9F46, 9F47

  • PubMed Abstract: 

    [FeFe]-hydrogenases catalyze the reversible two-electron reduction of two protons to molecular hydrogen. Although these enzymes are among the most efficient H 2 -converting biocatalysts in nature, their catalytic cofactor (termed H-cluster) is irreversibly destroyed upon contact with dioxygen. The [FeFe]-hydrogenase CbA5H from Clostridium beijerinckii has a unique mechanism to protect the H-cluster from oxygen-induced degradation. The protective strategy of CbA5H was proposed based on a partial protein structure of CbA5H's oxygen-shielded form. Here, we present a cryo-EM structure of 2.2 Å resolution from the entire enzyme in its dimeric and active state and elucidate the structural parameters of the reversible cofactor protection mechanism. We found that both subunits of the homodimeric structure of CbA5H have a Zn 2+ -binding four-helix domain, which does not play a role in electron transport as described for other complex protein structures. Biochemical data instead confirm that two [4Fe-4S] clusters are responsible for electron transfer in CbA5H, while the identified zinc atom is critical for oligomerization and protein stability.


  • Organizational Affiliation
    • Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44801, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[FeFe]-hydrogenase
A, B
674Clostridium beijerinckiiMutation(s): 0 
UniProt
Find proteins for A0A1I9RYV3 (Clostridium beijerinckii)
Explore A0A1I9RYV3 
Go to UniProtKB:  A0A1I9RYV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I9RYV3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
402 (Subject of Investigation/LOI)
Query on 402

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
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 
D [auth A]
E [auth A]
F [auth A]
O [auth B]
P [auth B]
D [auth A],
E [auth A],
F [auth A],
O [auth B],
P [auth B],
Q [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
R [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.298 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169α = 90
b = 169β = 90
c = 127γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
Japan Science and TechnologyJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references, Structure summary