Summary: Iron hydrogenase small subunit
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Iron hydrogenase small subunit Provide feedback
This family represents the small subunit of the Fe-only hydrogenases EC:18.104.22.168. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold .
Nicolet Y, Piras C, Legrand P, Hatchikian CE, Fontecilla-Camps JC; , Structure Fold Des 1999;7:13-23.: Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. PUBMED:10368269 EPMC:10368269
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This tab holds annotation information from the InterPro database.
InterPro entry IPR003149
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 [PUBMED: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 [PUBMED:10368269].
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Curation and family details
|Seed source:||Pfam-B_3750 (release 5.2)|
|Author:||Bateman A, Mian N, Griffiths-Jones SR|
|Number in seed:||109|
|Number in full:||999|
|Average length of the domain:||58.20 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||10.86 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Fe_hyd_SSU domain has been found. There are 10 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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