Homologous Superfamily

Iron hydrogenase, small subunit HydB-type (IPR008953)

Short name: Fe_hydrogenase_HydB

Overlapping entries


Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production.

Fe only hydrogenases (EC: show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters [PMID: 11921392]. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein.

The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold [PMID: 10368269].

The localisation of iron hydrogenases can be cytoplasmic or periplasmic. Periplasmic iron hydrogenases in Desulfovibrio consists of a large subunit (HydA) and a small subunit (HydB) [PMID: 2661538].

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0009055 electron transfer activity
GO:0008901 ferredoxin hydrogenase activity
GO:0005506 iron ion binding
GO:0051536 iron-sulfur cluster binding

Cellular Component

GO:0042597 periplasmic space

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.