5OK4 image
Deposition Date 2017-07-25
Release Date 2018-05-16
Last Version Date 2024-01-17
Entry Detail
PDB ID:
5OK4
Keywords:
Title:
Crystal structure of native [Fe]-hydrogenase Hmd from Methanothermobacter marburgensis inactivated by O2.
Biological Source:
Method Details:
Experimental Method:
Resolution:
1.29 Å
R-Value Free:
0.14
R-Value Work:
0.12
R-Value Observed:
0.12
Space Group:
H 3 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:5,10-methenyltetrahydromethanopterin hydrogenase
Gene (Uniprot):hmd
Chain IDs:A
Chain Length:344
Number of Molecules:1
Biological Source:Methanothermobacter marburgensis str. Marburg
Primary Citation
Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates.
Angew. Chem. Int. Ed. Engl. 57 4917 4920 (2018)
PMID: 29462510 DOI: 10.1002/anie.201712293

Abstact

Mono-iron hydrogenase ([Fe]-hydrogenase) reversibly catalyzes the transfer of a hydride ion from H(2) to methenyltetrahydromethanopterin (methenyl-H(4) MPT(+) ) to form methylene-H(4) MPT. Its iron guanylylpyridinol (FeGP) cofactor plays a key role in H(2) activation. Evidence is presented for O(2) sensitivity of [Fe]-hydrogenase under turnover conditions in the presence of reducing substrates, methylene-H(4) MPT or methenyl-H(4) MPT(+) /H(2) . Only then, H(2) O(2) is generated, which decomposes the FeGP cofactor; as demonstrated by spectroscopic analyses and the crystal structure of the deactivated enzyme. O(2) reduction to H(2) O(2) requires a reductant, which can be a catalytic intermediate transiently formed during the [Fe]-hydrogenase reaction. The most probable candidate is an iron hydride species; its presence has already been predicted by theoretical studies of the catalytic reaction. The findings support predictions because the same type of reduction reaction is described for ruthenium hydride complexes that hydrogenate polar compounds.

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