SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein bL31 superfamily (Ribosomal_bL31_sf)
Type: Homologous_superfamily

This superfamily represents the ribosomal protein bL31, a protein of the large ribosomal subunit found in bacteria and chloroplast.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ (Nuo/plastoQ_OxRdtase_6_NuoJ)
Type: Homologous_superfamily

This entry represents chain 6 from NADH:ubiquinone oxidoreductase and NADH-plastoquinone oxidoreductase. Bacterial proton-translocating NADH-quinone oxidoreductase (NDH-1) is composed of 14 different subunits. The chain belonging to this family is a subunit that constitutes the membrane sector of the complex. It reduces ubiquinone to ubiquinol utilising NADH. Plant chloroplastic NADH-plastoquinone oxidoreductase reduces plastoquinone to plastoquinol. Mitochondrial NADH-ubiquinone oxidoreductase from a variety of sources reduces ubiquinone to ubiquinol.

Subunit NuoJ has an unusual non-globular fold: three linearly arranged amino-terminal TM helices border NuoK, and TMs 4 and 5 are separated at the opposite sides of the domain. Thus, NuoJ interweaves between NuoK, A and N, stabilising the complex. TM3 of NuoJ contains in its middle a pi-bulge/kink, so this helix is probably flexible and mechanistically important. TM3 is the most conserved helix in NuoJ and is a hotspot for human mitochondrial disease mutations .
DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily (DNA-dir_RNA_pol_bsu_ext_1_sf)
Type: Homologous_superfamily

RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This superfamily represents a domain found in prokaryotic polymerases that spans the gap between domains 4 and 5 of the protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region .
GTPase HflX, N-terminal domain superfamily (GTPase_HflX_N_sf)
Type: Homologous_superfamily

This domain represents the N-terminal region of GTP-binding HflX-like proteins . These proteins interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP . The N-terminal region is necessary for stability of the whole protein, its structure is composed of four parallel β-strand and four α-helices.
Adenylosuccinate synthetase, domain 1 (Adenylosuccinate_synth_dom1)
Type: Homologous_superfamily

Adenylosuccinate synthetase (

) plays an important role in purine biosynthesis, by catalysing the GTP-dependent conversion of IMP and aspartic acid to AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-phosphate group of GTP is transferred to the 6-oxygen atom of IMP. An aspartate then displaces this 6-phosphate group to form the product adenylosuccinate. Adenylosuccinate synthetase has been characterised from various sources ranging from Escherichia coli (gene purA) to vertebrate tissues. In vertebrates, two isozymes are present: one involved in purine biosynthesis and the other in the purine nucleotide cycle.

The crystal structure of adenylosuccinate synthetase from E. coli reveals that the dominant structural element of each monomer of the homodimer is a central β-sheet of 10 strands. The first nine strands of the sheet are mutually parallel with right-handed crossover connections between the strands. The 10th strand is antiparallel with respect to the first nine strands. In addition, the enzyme has two antiparallel β-sheets, comprised of two strands and three strands each, 11 α-helices and two short 3/10-helices. Further, it has been suggested that the similarities in the GTP-binding domains of the synthetase and the p21ras protein are an example of convergent evolution of two distinct families of GTP-binding proteins . Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana when compared with the known structures from E. coli reveals that the overall fold is very similar to that of the E. coli protein .

This superfamily represents the domain 1 found in adenylosuccinate synthetase.
Adenylosuccinate synthetase, domain 2 (Adenylosuccinate_synth_dom2)
Type: Homologous_superfamily

Adenylosuccinate synthetase (

) plays an important role in purine biosynthesis, by catalysing the GTP-dependent conversion of IMP and aspartic acid to AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-phosphate group of GTP is transferred to the 6-oxygen atom of IMP. An aspartate then displaces this 6-phosphate group to form the product adenylosuccinate. Adenylosuccinate synthetase has been characterised from various sources ranging from Escherichia coli (gene purA) to vertebrate tissues. In vertebrates, two isozymes are present: one involved in purine biosynthesis and the other in the purine nucleotide cycle.

The crystal structure of adenylosuccinate synthetase from E. coli reveals that the dominant structural element of each monomer of the homodimer is a central β-sheet of 10 strands. The first nine strands of the sheet are mutually parallel with right-handed crossover connections between the strands. The 10th strand is antiparallel with respect to the first nine strands. In addition, the enzyme has two antiparallel β-sheets, comprised of two strands and three strands each, 11 α-helices and two short 3/10-helices. Further, it has been suggested that the similarities in the GTP-binding domains of the synthetase and the p21ras protein are an example of convergent evolution of two distinct families of GTP-binding proteins . Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana when compared with the known structures from E. coli reveals that the overall fold is very similar to that of the E. coli protein .

This superfamily represents the domain 2 found in adenylosuccinate synthetase.
Adenylosuccinate synthetase, domain 3 (Adenylosuccinate_synth_dom3)
Type: Homologous_superfamily

Adenylosuccinate synthetase (

) plays an important role in purine biosynthesis, by catalysing the GTP-dependent conversion of IMP and aspartic acid to AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-phosphate group of GTP is transferred to the 6-oxygen atom of IMP. An aspartate then displaces this 6-phosphate group to form the product adenylosuccinate. Adenylosuccinate synthetase has been characterised from various sources ranging from Escherichia coli (gene purA) to vertebrate tissues. In vertebrates, two isozymes are present: one involved in purine biosynthesis and the other in the purine nucleotide cycle.

The crystal structure of adenylosuccinate synthetase from E. coli reveals that the dominant structural element of each monomer of the homodimer is a central β-sheet of 10 strands. The first nine strands of the sheet are mutually parallel with right-handed crossover connections between the strands. The 10th strand is antiparallel with respect to the first nine strands. In addition, the enzyme has two antiparallel β-sheets, comprised of two strands and three strands each, 11 α-helices and two short 3/10-helices. Further, it has been suggested that the similarities in the GTP-binding domains of the synthetase and the p21ras protein are an example of convergent evolution of two distinct families of GTP-binding proteins . Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana when compared with the known structures from E. coli reveals that the overall fold is very similar to that of the E. coli protein .

This superfamily represents the domain 3 found in adenylosuccinate synthetase.
Phosphate acetyltransferase, domain 2 (P_AcTrfase_dom2)
Type: Homologous_superfamily

This superfamily represents the domain 2 found in phosphate acetyltransferase.

Phosphotransacetylase (

) catalyses reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate .

The Phosphotransacetylase enzyme is composed of six monomers per asymmetric unit. Each monomer has an α/β structure and consists of two domains (I and II). Domain I forms an α-β-α structure, with a strictly parallel five-stranded β-sheet in the middle 'sandwiched' by α-helices on each side. It contains the N- and C-terminal segments, a lactate dehydrogenase (LDH)-like nucleotide-binding fold (Rossmann fold), and a helical subdomain consisting of four α-helices. Domain II also adopts a typical α-β-α sandwich structure with a mixed six-stranded β-sheet that is embraced by three helices on one side and two helices on the other side. The two domains are separated by a distinct cleft .
Phosphate acetyltransferase, domain 1 (P_AcTrfase_dom1)
Type: Homologous_superfamily

Phosphotransacetylase (

) catalyses reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate .

The Phosphotransacetylase enzyme is composed of six monomers per asymmetric unit. Each monomer has an α/β structure and consists of two domains (I and II). Domain I forms an α-β-α structure, with a strictly parallel five-stranded β-sheet in the middle 'sandwiched' by α-helices on each side. It contains the N- and C-terminal segments, a lactate dehydrogenase (LDH)-like nucleotide-binding fold (Rossmann fold), and a helical subdomain consisting of four α-helices. Domain II also adopts a typical α-β-α sandwich structure with a mixed six-stranded β-sheet that is embraced by three helices on one side and two helices on the other side. The two domains are separated by a distinct cleft .

This superfamily represents the domain 1 found in phosphate acetyltransferase.
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C-terminal, domain 1 (GatB_C_1)
Type: Homologous_superfamily

Glutamyl-tRNA(Gln) amidotransferase (Gat;

) provides a means of producing correctly charged Gln-tRNA(Gln) through the transamidation of mis-acylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase . The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The enzyme is composed of three subunits: A (an amidase), B and C. It also exists in eukaryotes as a protein targeted to the mitochondria.

The heterotrimer GatABC is involved in converting Glu to Gln and/or Asp to Asn, when the amino acid is attached to the appropriate tRNA. In Lactobacillus, GatABC is responsible for producing tRNA(Gln). In Archaea, GatABC is responsible for producing tRNA(Asn), while GatDE is responsible for producing tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyses both tRNA(Gln) and tRNA(Asn).

This entry represents the first α-helical subdomain found in the C-terminal structural domain of GatB and GatE subunits.
Primosomal protein N', 3' DNA-binding domain superfamily (PriA_3primeBD_sf)
Type: Homologous_superfamily

Primosomal protein N', also known as ATP-dependent DNA helicase PriA, is a component of the primosome, involved in replication, repair and recombination. PriA is a multifunctional enzyme that mediates the essential process of restarting prematurely terminated DNA replication reactions in bacteria . PriA presents a two-domain architecture, with an N-terminal DNA-binding domain (DBD) and a C-terminal helicase domain (HD). Structural studies reveal a central helicase core surrounded by an array of DNA-binding elements. These elements include two domains within the DBD, a 3' DNA-binding domain (3'BD) and an unusual circularly permuted winged helix (WH) domain, and two domains within the HD, a Cys-rich region (CRR) that binds two Zn2+ ions and a C-terminal domain (CTD) which shows unexpected similarity to the S10 subunit of the bacterial ribosome .

This superfamily represents the 3' DNA binding domain.
GTP-binding protein TypA/BipA, C-terminal (TypA/BipA_C)
Type: Homologous_superfamily

The translational GTPase BipA (also known as TypA or YihK) regulates the expression of virulence and pathogenicity factors in several eubacteria. BipA-dependent expression of virulence factors occurs under starvation conditions, such as encountered during infection of a host. BipA is composed of five domains. Domain I consists of a central six-stranded β-sheet surrounded by five α-helices, which is characteristic for the G domain found in translational GTPases. Domain II has the distinctive OB-fold of oligonucleotide/oligosaccharide binding domains. Domains III and V both have the same double-split β-α-β fold. The C-terminal domain of BipA spatially occupies a position between domains III and V and consists of a unique mixed α+β fold composed of eight β-sheets and two α-helices .

This superfamily represents the C-terminal domain found in GTP-binding protein TypA/BipA.
QueA, domain 1 (QueA_dom1)
Type: Homologous_superfamily

This entry represents the S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA. Queuosine is a hypermodified nucleoside that usually occurs in the first position of the anticodon of tRNAs specifying the amino acids asparagine, aspartate, histidine, and tyrosine. The hypermodified nucleoside is found in bacteria and eukaryotes . Queuosine is synthesized
de novo
exclusively in bacteria; for eukaryotes the compound is a nutrient factor. Queuosine biosynthesis protein, or S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (QueA) catalyses the formation of the 2,3-epoxy-4,5-dihydroxycyclopentane ring of the Q precursor epoxyqueuosine (oQ). S-adenosyl-L-methionine (AdoMet) reacts with 7-aminomethyl-7-deazaguanine of tRNA at position 34 to yield adenine, methionine, and a modified tRNA with oQ at position 34.

QueA consists of two domains: domain 1 has three layers (α/β/α)), while domain 2 is a closed β-barrel with Greek-key topology .

This superfamily represents the domain 1 found in S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA.
QueA, domain 2 (QueA_dom2)
Type: Homologous_superfamily

This entry represents the S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA. Queuosine is a hypermodified nucleoside that usually occurs in the first position of the anticodon of tRNAs specifying the amino acids asparagine, aspartate, histidine, and tyrosine. The hypermodified nucleoside is found in bacteria and eukaryotes . Queuosine is synthesized
de novo
exclusively in bacteria; for eukaryotes the compound is a nutrient factor. Queuosine biosynthesis protein, or S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (QueA) catalyses the formation of the 2,3-epoxy-4,5-dihydroxycyclopentane ring of the Q precursor epoxyqueuosine (oQ). S-adenosyl-L-methionine (AdoMet) reacts with 7-aminomethyl-7-deazaguanine of tRNA at position 34 to yield adenine, methionine, and a modified tRNA with oQ at position 34.

QueA consists of two domains: domain 1 has three layers (α/β/α)), while domain 2 is a closed β-barrel with Greek-key topology .

This superfamily represents the domain 2 found in S-adenosylmethionine:tRNA ribosyltransferase-isomerase, QueA.
MutL, C-terminal domain, dimerisation subdomain (MutL_C_dimsub)
Type: Homologous_superfamily

The protein MutL is essential in mismatch repair as it coordinating multiple protein-protein interactions that signal strand removal upon mismatch recognition by MutS. MutL is composed of two structurally conserved domains connected by a variable flexible linker: an N-terminal ATPase domain and C-terminal dimerisation domain . The latter harbours the the endonuclease activity of the protein. Structural studies have shown that this C-terminal region is organized into a dimerization and a regulatory subdomain connected by a helical lever spanning the conserved endonuclease motif.

This superfamily represents the dimerization subdomain of the C-terminal domain of the MutL protein which presents a Zn2+ binding site and is important for the mismatch repair function of MutL .
MutL, C-terminal domain, regulatory subdomain (MutL_C_regsub)
Type: Homologous_superfamily

The protein MutL is essential in mismatch repair as it coordinating multiple protein-protein interactions that signal strand removal upon mismatch recognition by MutS. MutL is composed of two structurally conserved domains connected by a variable flexible linker: an N-terminal ATPase domain and C-terminal dimerisation domain . The latter harbours the the endonuclease activity of the protein. Structural studies have shown that this C-terminal region is organized into a dimerization and a regulatory subdomain connected by a helical lever spanning the conserved endonuclease motif.

This superfamily represents the regulatory subdomain of the C-terminal domain of the MutL protein .
Serine acetyltransferase, N-terminal domain superfamily (Ser_AcTrfase_N_sf)
Type: Homologous_superfamily

Serine acetyltransferase (SAT) catalyzes the first step of cysteine synthesis in microorganisms and higher plants. SAT is composed of two domains: an N-terminal α-helical domain, comprising eight α-helices, and left-handed C-terminal β-helical domain, comprising of fourteen β-strands forming five coils of the helix .

This superfamily represents the N-terminal domain found in serine acetyltransferase.
Zip3/RNF212-like (Zip3/RNF212-like)
Type: Family

This entry represents budding yeast Zip3 (also known as Cst9) and its homologues including Vilya/Nenya/narya from Drosophila melanogaster, RNF212/RNF212B from animals and Zip homologous proteins 1, 2, 3 and 4 from Caenorhabditis elegans. In budding yeasts, Zip3 is a SUMO E3 ligase and a component of the synapsis initiation complex (SIC) required for synaptonemal complex formation. Zip3 possesses a C3H2C3 RING finger motif, which is required for its E3 SUMO ligase activity in vitro .

The synaptonemal complex (SC) is a proteinaceous complex that apparently mediates synapsis between homologous chromosomes during meiotic prophase . A number of chromosomal crossover factors and DNA damage repair components have been found to associate with both synaptonemal complexes and multiple synaptonemal complexes (polycomplexes). These include Zip3 (Cst9) from budding yeast, which localizes throughout the body of polycomplexes .
Small integral membrane protein 11 (SMIM11)
Type: Family

This entry includes small integral membrane protein 11A and 11B from vertebrates. The function of these proteins is not clear.
Transmembrane protein 45 (TMEM45)
Type: Family

This family consists of transmembrane proteins 45A and 45B. Their function is not known.
NuoE domain (NuoE_dom)
Type: Domain

NADH:ubiquinone oxidoreductase (Nuo), also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24kDa subunit of Complex 1 .

This entry represents the C-terminal domain of NuoE, also found in formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases. A subset of these proteins contain both NuoE and NuoF in a single chain.
SNX7, PX domain (PX_SNX7)
Type: Domain

Sorting nexin-7 (SNX7) belongs to the sorting nexin family, which contains a conserved PX (phox homology) domain that is responsible for binding to specific phosphoinositides . It may be involved in several stages of intracellular trafficking.

The Phox Homology (PX) domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds phosphoinositides (PIs) and targets the protein to PI-enriched membranes . SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway .
SNX7, BAR domain (BAR_SNX7)
Type: Domain

Sorting nexin-7 (SNX7) belongs to the sorting nexin family, which contains a conserved PX (phox homology) domain that is responsible for binding to specific phosphoinositides . It may be involved in several stages of intracellular trafficking.

This entry represents the BAR domain found in sorting nexin-7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions .
Ribosomal protein S6 kinase delta-1, PX domain (PX_S6K-delta-1)
Type: Domain

This entry represents the PX domain found in ribosomal protein S6 kinase delta-1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others .

Ribosomal protein S6 kinase delta-1, also known as RPK118, binds sphingosine kinase-1, a key enzyme in the synthesis of the lipid messenger sphingosine 1 phosphate (SPP). It may be involved in transmitting SPP-mediated signaling into the cell . RPK118 specifically binds to phosphatidylinositol 3-phosphate . RPK118 also binds peroxiredoxin-3 and may be involved in transporting peroxiredoxin-3 from the cytoplasm to its mitochondrial site of function via endosome trafficking . The C terminus of RPK118 consist of a domain with conserved Ser/Thr protein kinase residues, specially resembling human ribosome protein S6 kinase .