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Structure paper

TitleStructural determinants of oxygen resistance and Zn-mediated stability of the [FeFe]-hydrogenase from .
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 122, Issue 3, Page e2416233122, Year 2025
Publish dateJan 21, 2025
AuthorsJifu Duan / Andreas Rutz / Akihiro Kawamoto / Shuvankar Naskar / Kristina Edenharter / Silke Leimkühler / Eckhard Hofmann / Thomas Happe / Genji Kurisu /
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-converting biocatalysts in nature, their ...[FeFe]-hydrogenases catalyze the reversible two-electron reduction of two protons to molecular hydrogen. Although these enzymes are among the most efficient H-converting biocatalysts in nature, their catalytic cofactor (termed H-cluster) is irreversibly destroyed upon contact with dioxygen. The [FeFe]-hydrogenase CbA5H from 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-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.
External linksProc Natl Acad Sci U S A / PubMed:39805018 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.21 - 2.9 Å
Structure data

60383

8zqd

EMDB-60383, PDB-8zqd:
Anaerobically isolated active [FeFe]-hydrogenase CbA5H
Method: EM (single particle) / Resolution: 2.21 Å

PDB-9f46:
crystal structure of apo-[FeFe]-hydrogenase CbA5H from Clostridium beijerinckii
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

PDB-9f47:
crystal structure of [FeFe]-hydrogenase CbA5H from Clostridium beijerinckii in Hinact state
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-402:
dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)

ChemComp-CL:
Unknown entry

ChemComp-HOH:
WATER

Source
  • clostridium beijerinckii (bacteria)
KeywordsOXIDOREDUCTASE / [FeFe]-hydrogenases / homodimer / Zn-binding / [FeFe]-hydrogenase / apo / Clostridium beijerinckii / inactive state

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