9R6Z image
Deposition Date 2025-05-13
Release Date 2025-10-22
Last Version Date 2025-10-22
Entry Detail
PDB ID:
9R6Z
Keywords:
OXIDOREDUCTASE
Title:
Cubic state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus
Biological Source:
Source Organism:
Methanothermococcus thermolithotrophicus DSM 2095 (Taxon ID: 523845)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.85 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 3
9R6Z validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:F420-reducing [NiFe]-hydrogenase subunit alpha
Chain IDs:A, D, G, J
Chain Length:410
Number of Molecules:4
Biological Source:Methanothermococcus thermolithotrophicus DSM 2095
Polymer Type:polypeptide(L)
Molecule:F420-reducing [NiFe]-hydrogenase subunit beta
Chain IDs:B, E, H, K
Chain Length:282
Number of Molecules:4
Biological Source:Methanothermococcus thermolithotrophicus DSM 2095
Polymer Type:polypeptide(L)
Molecule:F420-reducing [NiFe]-hydrogenase subunit gamma
Chain IDs:C, F, I, L
Chain Length:241
Number of Molecules:4
Biological Source:Methanothermococcus thermolithotrophicus DSM 2095
Ligand Molecules
FAD
GOL
NFU
SF4
SO4
Primary Citation
Structural and Spectroscopic Insights into Catalytic Intermediates of a [NiFe]-hydrogenase from Group 3.
Chembiochem ? e202500692 e202500692 (2025)
PMID: 41078086 DOI: 10.1002/cbic.202500692

Abstact

Hydrogenases catalyze reversible H2 production and are potential models for renewable energy catalysts. Here, the full redox landscape of a group 3 [NiFe]-hydrogenase from methanothermococcus thermolithotrophicus is elucidated, resembling group 1 enzymes. Structural and spectroscopic analyses reveal a catalytic-ready state with nickel seesaw coordination, enabling intermediate trapping and advancing mechanistic understanding of oxygen-sensitive [NiFe] enzymes.

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Primary Citation of related structures
9R6Z