Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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Fe_hyd_SSU Iron hydrogenase small subunit

SMART accession number:	SM00902
Description:	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 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).
Interpro abstract (IPR003149):	This family represents the small subunit of the Fe-only hydrogenases ( EC 1.18.99.1 ). The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold [ (PUBMED:10368269) ].
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 4428 Fe_hyd_SSU domains in 4426 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing Fe_hyd_SSU domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Fe_hyd_SSU domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing Fe_hyd_SSU domain in the selected taxonomic class.

• Cellular role (predicted cellular role)

• Cellular role: metabolism
  

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Frey M
  • Hydrogenases: hydrogen-activating enzymes.
  • Chembiochem. 2002; 3: 153-60

  • Nicolet Y, Piras C, Legrand P, Hatchikian CE, Fontecilla-Camps JC
  • Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusualcoordination to an active site Fe binuclear center.
  • Structure. 1999; 7: 13-23
  • Display abstract

  • BACKGROUND: Many microorganisms have the ability to either oxidizemolecular hydrogen to generate reducing power or to produce hydrogen inorder to remove low-potential electrons. These reactions are catalyzed bytwo unrelated enzymes: the Ni-Fe hydrogenases and the Fe-onlyhydrogenases. RESULTS: We report here the structure of the heterodimericFe-only hydrogenase from Desulfovibrio desulfuricans - the first for thisclass of enzymes. With the exception of a ferredoxin-like domain, thestructure represents a novel protein fold. The so-called H cluster of theenzyme is composed of a typical [4Fe-4S] cubane bridged to a binuclearactive site Fe center containing putative CO and CN ligands and onebridging 1, 3-propanedithiol molecule. The conformation of the subunitscan be explained by the evolutionary changes that have transformedmonomeric cytoplasmic enzymes into dimeric periplasmic enzymes. Plausibleelectron- and proton-transfer pathways and a putative channel for theaccess of hydrogen to the active site have been identified. CONCLUSIONS:The unrelated active sites of Ni-Fe and Fe-only hydrogenases have severalcommon features: coordination of diatomic ligands to an Fe ion; a vacantcoordination site on one of the metal ions representing a possiblesubstrate-binding site; a thiolate-bridged binuclear center; and plausibleproton- and electron-transfer pathways and substrate channels. Thediatomic coordination to Fe ions makes them low spin and favors low redoxstates, which may be required for catalysis. Complex electron paramagneticresonance signals typical of Fe-only hydrogenases arise from magneticinteractions between the [4Fe-4S] cluster and the active site binuclearcenter. The paucity of protein ligands to this center suggests that it wasimported from the inorganic world as an already functional unit.

• Structure (3D structures containing this domain)

• 3D Structures of Fe_hyd_SSU domains in PDB

  PDB code	Main view	Title
  1c4a		BINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE OF THE FE-ONLY HYDROGENASE (CPI) FROM CLOSTRIDIUM PASTEURIANUM
  1c4c		BINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE OF THE FE-ONLY HYDROGENASE (CPI) FROM CLOSTRIDIUM PASTEURIANUM
  1e08		Structural model of the [Fe]-Hydrogenase/cytochrome c553 complex combining NMR and soft-docking
  1feh		FE-ONLY HYDROGENASE FROM CLOSTRIDIUM PASTEURIANUM
  1gx7		Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase
  1hfe		1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS
  2n0s		2N0S
  3c8y		1.39 Angstrom crystal structure of Fe-only hydrogenase
  3lx4		Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG)
  4r0v		4R0V
  4xdc		4XDC
  4xdd		4XDD
  5byq		5BYQ
  5byr		5BYR
  5bys		5BYS

• Links (links to other resources describing this domain)

• PFAM	Fe_hyd_SSU
  INTERPRO	IPR003149

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