SII-SWORD/CoKE huggingface dataset:
Superantigen toxin, C-terminal (SuperAg_toxin_C)
Type: Homologous_superfamily

This entry represents superantigen toxins from Staphylococcus aureus and Streptococcus pyogenes, which share a common core structure consisting of β(2)-α-β(2). S. aureus toxins with this fold include: enterotoxins A (SEA) , B (SEB) , C2 (SEC2) , C3 (SEC3) and H (SEH) , heat shock syndrome toxin-1 , and superantigen-like proteins SET1 and SET3 . S. pyogenes toxins with this fold include: pyrogenic exotoxins A1 and Spe-J , and in superantigen proteins Spe-C , Spe-H , Smez-2 and SSA .
MIR motif (MIR_motif)
Type: Domain

The MIR domain is named after three of the proteins in which it occurs: protein Mannosyltransferase (

), Inositol 1,4,5-trisphosphate receptor (IP3R) and Ryanodine receptor (RyR). MIR domains have also been found in eukaryotic stromal cell-derived factor 2 (SDF-2) and in Chlamydia trachomatis protein CT153. The MIR domain may have a ligand transferase function. This domain has a closed β-barrel structure with a hairpin triplet, and has an internal pseudo-threefold symmetry. The MIR motifs that make up the MIR domain consist of ~50 residues and are often found in multiple copies.

Inositol 1,4,5-trisphosphate (InsP3) is an intracellular second messenger that transduces growth factor and neurotransmitter signals. InsP3 mediates the release of Ca
2+
from intracellular stores by binding to specific Ca
2+
channel-coupled receptors. Ryanodine receptors are involved in communication between transverse-tubules and the sarcoplamic reticulum of cardiac and skeletal muscle. The proteins function as a Ca
2+
-release channels following depolarisation of transverse-tubules . The function is modulated by Ca
2+
, Mg2+, ATP and calmodulin. Deficiency in the ryanodine receptor may be the cause of malignant hyperthermia (MH) and of central core disease of muscle (CCD) . protein O-mannosyltransferases transfer mannose from DOL-P-mannose to ser or thr residues on proteins.
Large ribosomal subunit protein uL1, 3-layer alpha/beta-sandwich domain (Ribosomal_uL1_3-a/b-sand)
Type: Homologous_superfamily

Ribosomal protein uL1 is the largest protein from the large ribosomal subunit. The uL1 protein contains two domains: 2-layer α/β domain and a 3-layer α/β domain (interrupts the first domain). This entry represents the 3-layer domain.

It has been shown that the 2-layer α/β-sandwich domain is for RNA binding. The 3-layer α/β domain is to stabilise the uL1-rRNA complex . The 3-layer domain of ribosomal protein TthL1 hinders binding of intact protein with RNA due to interdomain flexibility. As a result, the rate of complex formation with mRNA increases for the isolated domain I as compared with that for intact TthL1 .
Domain of unknown function DUF695 (DUF695)
Type: Domain

This domain is found at the N terminus of a number of bacterial proteins of unknown function.
Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal (CAP/MinC_C)
Type: Homologous_superfamily

Cyclase-associated proteins (CAPs) are highly conserved monomeric actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways . Only yeast CAPs are involved in adenylate cyclase activation. The C-terminal domain of CAP proteins is responsible for G-actin-binding that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes.

In Escherichia coli, three Min proteins (MinC, MinD and MinE) negatively regulate FtsZ assembly at the cell poles in order to ensure the Z-ring only assembles at cell midpoint. MinC inhibits formation of the Z-ring by preventing FtsZ assembly. MinD binds to MinC near the cell poles, sequestering MinC away from the cell midpoint so the Z-ring can form there. MinC is an oligomer, probably a dimer, that consists of two domains: the N-terminal domain is responsible for FtsZ inhibition, while the C-terminal domain is responsible for binding to MinD and to a component of the division septum .

This entry represents a structural domain found at the C-terminal of CAP proteins as well as MinC. This domain has a superhelical structure, where the superhelix turns are made of either two (CAP) or three (MinC) β-strands each.
Prismane-like, alpha/beta-sandwich (Prismane-like_a/b-sand)
Type: Homologous_superfamily

Prismane (hybrid-cluster) proteins, also known as hydroxylamine reductases, are present in a wide range of bacteria and archaea, and are characterised by their two Fe/S centres: a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster . Prismane proteins contain four domains: two spectrin repeat-like 3-helical bundle domains, and two α/β domains with Rossmann-fold topology. Several proteins are structurally related to prismane, including Ni-containing carbon monoxide dehydrogenase (CODH) (lack one of the N-terminal 3-helical bundle domains), the alpha and beta subunits of bifunctional CODH, and the alpha and beta subunits of acetyl-CoA synthetase.

This entry represents the 3-layer (α/β/α) sandwich domain found in prismane, CODH, and in acetyl-CoA synthases.
Prismane, alpha-bundle (Prismane_a-bundle)
Type: Homologous_superfamily

Prismane (hybrid-cluster) proteins are present in a wide range of bacteria and archaea, and are characterised by their two Fe/S centres: a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster . Prismane proteins (hybrid cluster proteins) contain four domains: two spectrin repeat-like 3-helical bundle domains, and two α/β domains with Rossmann-fold topology.

This entry represents an α-bundle domain with an up-and-down topology found in prismane.
CO dehydrogenase, alpha-bundle (CO_DH_a-bundle)
Type: Homologous_superfamily

This superfamily represents an α-bundle domain with an up-and-down topology found in Ni-containing carbon monoxide dehydrogenases (CODH) (

). These enzymes reversibly oxidise CO to CO(2), and play key roles in the energy-yielding pathways of various autotrophic anaerobes, allowing these organisms to grow with CO as the sole carbon source . The active sites of these enzymes contain Ni-iron-sulphur (NiFeS) clusters. This family also includes the CODH subunit of bifunctional CODH/acetyl-CoA synthetase (CODH/ACS), which contains two Ni-containing active sites to catalyse the formation of acetyl-CoA from CO(2)-derived CO .
Succinyl-CoA synthetase-like (Succinyl-CoA_synth-like)
Type: Homologous_superfamily

This superfamily represents a structural domain consisting of 3-layers, α/β/α. This domain is found in both the alpha and beta chains of succinate--CoA ligase (also known as succinyl-CoA synthase;

(GDP-forming) and

(ADP-forming)) . This domain can also be found in ATP citrate synthase (

), malate-CoA ligase (

) and acetate-CoA ligase (or acetyl-CoA synthase) (

), as well as bacterial Fdr. Some members of the domain utilise ATP others use GTP.
ProQ/FinO domain (ProQ/FinO)
Type: Domain

This entry represents a structural domain consisting of six helices in an irregular non-globular array; it also contains two small β-hairpins. This domain is found at the C terminus of the RNA-binding fertility inhibitor FinO that represses the conjugative transfer of F-like plasmids in Escherichia coli. FinO blocks the translation of TraJ, a positive activator of transcription of gene thereby protecting it from degradation, and catalyses FinP-TraJ mRNA hybridization. Interactions between these two RNAs are predicted to block the TraJ ribosomal binding site. FinO is largely helical, binds to its highest affinity binding site within FinP as a monomer, and contains two distinct RNA binding regions .

This domain is also found as an N-terminal domain in ProQ, a protein required for full activation of the osmoprotectant transporter ProP in Escherichia coli .
Pyruvoyl-dependent histidine/arginine decarboxylase (Pyr-dep_his/arg-deCO2ase)
Type: Homologous_superfamily

This entry represents a structural domain found in pyruvoyl-dependent histidine decarboxylase (

) and arginine decarboxylase (

). This domain consists of a duplication of a β-α-β(2) motif that forms a 4-layer α/β/β/α topology, which contains a silk-like β-sandwich. This domain contains two chains resulting from self-processing of a single-chain precursor. These proteins form heterohexamers .

Histidine decarboxylase catalyses the formation of histamine from histidine. It requires a pyruvoyl group for its activity. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta) 6 by nonhydrolytic self-catalysis.

Arginine decarboxylase catalyses the interconversion of arginine and agmatine plus carbon dioxide. It requires a pyruvoyl group for its activity. Archaeoglobus fulgidus contains three copies of this 80-residue domain, all of which are very closely related.
Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain (Pyr-dep_his/arg-deCO2ase_sand)
Type: Homologous_superfamily

This entry represents a structural subdomain found in pyruvoyl-dependent histidine decarboxylase (

) and arginine decarboxylase (

). This subdomain consists of a 3-layer β-β-α sandwich. These proteins form heterohexamers .

Histidine decarboxylase catalyses the formation of histamine from histidine. It requires a pyruvoyl group for its activity. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta) 6 by nonhydrolytic self-catalysis.

Arginine decarboxylase catalyses the interconversion of arginine and agmatine plus carbon dioxide. It requires a pyruvoyl group for its activity.
Histidine decarboxylase proenzyme, N-terminal (Pyr-dep_his-deCO2ase_N)
Type: Homologous_superfamily

This entry represents a structural subdomain found at the N terminus in Histidine decarboxylase proenzyme. This subdomain has an irregular structure containing both β-strand and α-helical regions. These proteins form heterohexamers .

Histidine decarboxylase catalyses the formation of histamine from histidine. It requires a pyruvoyl group for its activity. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta) 6 by nonhydrolytic self-catalysis.
Adenovirus Pll, hexon, N-terminal (Adenovirus_Pll_hexon_N)
Type: Domain

Hexon is a major coat protein found in various species-specific Adenoviruses, which are type II dsDNA viruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices . The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a β-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions .

This entry represents the N-terminal domain of hexon coat proteins.
Adenovirus Pll, hexon, C-terminal (Adenovirus_Pll_hexon_C)
Type: Domain

Hexon is a major coat protein found in various species-specific Adenoviruses, which are type II dsDNA viruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices . The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a β-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions .

This entry represents the C-terminal domain of hexon coat proteins.
Adenovirus Pll, hexon, subdomain 3 (Adenovirus_Pll_hexon_sub3)
Type: Homologous_superfamily

Hexon is a major coat protein found in various species-specific Adenoviruses, which are type II dsDNA viruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices . The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a β-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions .

This entry represents a structural subdomain with a complex α/β topology.
Group II dsDNA virus coat/capsid protein (VP_dsDNA_II)
Type: Homologous_superfamily

Hexon is a major coat protein found in various species-specific Adenoviruses, which are type II dsDNA viruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices . The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a β-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions .

The major capsid proteins (vp54 and vp72) found in Iridoviruses, Phycodnaviruses, Asfarviruses and Ascoviruses share the same structure. All these viruses are type II dsDNA viruses with no RNA stage. This is the most abundant structural protein and can account for up to 45% of virion protein . The structure of vp54 has been determined from Paramecium bursaria Chlorella virus 1 (PBCV-1), a very large icosahedral virus containing an internal membrane enclosed within a glycoprotein coat. The vp54 protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. The vp54 protein forms a trimer, where the domains are arranged around a pseudo 6-fold axis. The domains have a β-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology .

Similarly, the major capsid protein p3 from Bacteriophage PRD1 also adopts a similar double-barrel structure comprising two eight-stranded viral β-barrels or jelly rolls, each of which contains a 12-residue α-helix. This protein then trimerises through a 'trimerisation loop' sequence, and is incorporated within the viral capsid .
Bacteriophage PRD1, P3, N-terminal (Phage_PRD1_P3_N)
Type: Homologous_superfamily

The major capsid protein P3 from Bacteriophage PRD1 adopts a double-barrel structure comprising two eight-stranded viral β-barrels or jelly rolls, each of which contains a 12-residue α-helix. This protein then trimerises through a 'trimerisation loop' sequence, and is incorporated within the viral capsid .
ArgJ-like domain superfamily (ArgJ-like_dom_sf)
Type: Homologous_superfamily

This superfamily represents a structural domain found in ArgJ, a bifunctional protein that catalyses the first (

) and fifth (

) steps in arginine biosynthesis . The domain also occurs in a number of proteins annotated as DmpA serine peptidases.
Bromoperoxidase/chloroperoxidase C-terminal (Br/Cl_peroxidase_C)
Type: Homologous_superfamily

This superfamily represents an α helical domain is found in bromoperoxidases and at the C-terminal of chloroperoxidases, both being haloperoxidases . The structure of chloroperoxidase from the fungus Curvularia inaequalis consists of a duplication containing two core α-helical bundles arranged as in other family dimers . Chloroperoxidases (

) use a haem cofactor to bring about the chlorination of a range of organic molecules, forming stable C-Cl bonds.

The vanadium-dependent haloperoxidases exclusively catalyse the oxidation of halides. Vanadium-dependent haloperoxidase has an almost all-helical structure, with two four-helix bundles and only three small β-sheets. The holoenzyme contains trigonal-bipyramidal coordinated vanadium atoms at its two active centres.
Signal transduction histidine kinase, sporulation regulator SpoOB (Sig_transdc_His_kin_SpoOB)
Type: Homologous_superfamily

Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions . Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk . These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more . Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) . The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.

A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response .

Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms . Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation , and CheA, which plays a central role in the chemotaxis system . Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water . The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily.

SpoOB is a response regulator that responds to nutritional stress by inducing sporulation. SpoOB is a phosphotransferase that acts upon SpoOA using SpoOF as the phosphor-donor. Phosphorylated SpoOA ca activate sporulation-specific gene transcription . SpoOB has an α-β core structure that resembles the histidine kinase fold, but lacks the kinase ATP-binding site .

Domains with a similar structure to that found in SpoOB are present in other sensor proteins, such as malate kinase sensor MalK (

), a member of a two-component regulatory system malK/malR that is involved in the activation of maeA, maeN and yflS in presence of malate .
Sporulation initiation phosphotransferase B, C-terminal (SpoOB_C)
Type: Domain

Response regulatory proteins such as sensor kinases control a variety of environmentally induced responses in bacteria. SpoOB is a response regulator that responds to nutritional stress by inducing sporulation. SpoOB is a phosphotransferase that acts upon SpoOA using SpoOF as the phosphor-donor. Phosphorylated SpoOA ca activate sporulation-specific gene transcription .

SpoOB has an α-β core structure that resembles the histidine kinase fold, but lacks the kinase ATP-binding site . This domain is found at the C teminus of SpoOB, as well as in other sensor kinases.
Mog1/PsbP, alpha/beta/alpha sandwich (Mog1/PsbP_a/b/a-sand)
Type: Homologous_superfamily

This entry represents a structural domain consisting of a 3-layer α/β/α fold. The β layer is composed of seven β-sheets, and the overall order is: (β-hairpin)-β(3)-α-β(4)-α. Domains with this structure are found in the following protein families:

Ran-binding protein Mog1, which interacts with Ran GTPase to stimulate guanine nucleotide release, suggesting Mog1 regulates the nuclear transport functions of Ran .

The photosystem II (PSII) oxygen-evolving complex protein PsbP, which is a regulator necessary for the biogenesis of optically active PSII. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions .
Peptidase C15, pyroglutamyl peptidase I-like (Peptidase_C15-like)
Type: Family

This group of cysteine peptidases belong to MEROPS peptidase family C15 (pyroglutamyl peptidase I, clan CF). The type example being pyroglutamyl peptidase I of Bacillus amyloliquefaciens. There are similarities in structure between members of clan CF and members of three clans of metallopeptidases (MC, MF and MH) and all four are included in the same superfamily (phosphorylase/hydrolase-like fold) by the SCOP database. Members of clan CF have an α/β/α sandwich fold .

Pyroglutamyl peptidase I (also known as pyrrolidone carboxyl peptidase, Pcp or PYRase) is an exopeptidase that hydrolytically removes the pGlu from pGlu-peptides or pGlu-proteins . PYRase has been found in prokaryotes and eukaryotes where at least two different classes have been characterised: the first containing bacterial and animal type I PYRases, and the second containing animal type II and serum PYRases. Type I and bacterial PYRases are soluble enzymes, while type II PYRases are membrane-bound. The primary application of PYRase has been its utilisation for protein or peptide sequencing, and bacterial diagnosis . The conserved residues Cys-144 and His-168 have been identified by inhibition and mutagenesis studies .

Pyroglutamyl-peptidase 1-like protein belongs to the petidase C15 family, though its exact function is not known.