ISDA: 9R5I

Deposition Date 2025-05-08

Release Date 2025-10-22

Last Version Date 2025-11-19

Entry Detail

PDB ID:

9R5I

Keywords:

OXIDOREDUCTASE

Title:

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 3

Biological Source:

Source Organism:

Methanothermococcus thermolithotrophicus DSM 2095 (Taxon ID: 523845)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.13 Å

R-Value Free:

0.20

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 31 2 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit alpha
Chain IDs:A, D
Chain Length:410
Number of Molecules:2
Biological Source:Methanothermococcus thermolithotrophicus DSM 2095

UniProt ID:Q60338 Pfam ID:PF00374

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit beta
Chain IDs:B, F
Chain Length:282
Number of Molecules:2
Biological Source:Methanothermococcus thermolithotrophicus DSM 2095

UniProt ID:Q60341 Pfam ID:PF04422, PF04432

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit gamma
Chain IDs:C, E
Chain Length:241
Number of Molecules:2
Biological Source:Methanothermococcus thermolithotrophicus DSM 2095

UniProt ID:Q60340 Pfam ID:PF01058, PF00037

Ligand Molecules

EDO

FAD

FES

GOL

MES

NFU

PE4

SF4

SO4

Primary Citation

Structural and Spectroscopic Insights into Catalytic Intermediates of a [NiFe]-hydrogenase from Group 3.

Jespersen, M, Lorent, C, Lemaire, O.N, Zebger, I, Wagner, T.Show

Chembiochem 26 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

Abstact

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