SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein bL31 type A (Ribosomal_bL31_A)
Type: Family

This entry represents 50S ribosomal protein bL31 from the type A subfamily.

Ribosomal protein bL31 is one of the proteins from the large ribosomal subunit. bL31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.

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 .
Dual-specificity RNA methyltransferase RlmN (RNA_MTrfase_RlmN)
Type: Family

Dual-specificity RNA methyltransferase RlmN specifically methylates position 2 of adenine 2503 in 23S rRNA, which serves to optimize ribosomal fidelity, and position 2 of adenine 37 in tRNAs. Unmodified tRNA is not a suitable substrate for RlmN, which suggests that RlmN works in a late step during tRNA maturation .
Large ribosomal subunit protein bL31 type B (Ribosomal_bL31_B)
Type: Family

This entry represents 50S ribosomal protein bL31 from the type B subfamily.

Ribosomal protein bL31 is one of the proteins from the large ribosomal subunit. bL31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.

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 .
Thiamine thiazole synthase (Sti35)
Type: Family

This entry represents the thiamine thiazole synthase, which is involved in biosynthesis of the thiamine precursor thiazole in fungi and in chloroplasts. It catalyses the conversion of NAD and glycine to adenosine diphosphate 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylic acid (ADT), an adenylated thiazole intermediate. The reaction includes an iron-dependent sulfide transfer from a conserved cysteine residue of the protein to a thiazole intermediate. The enzyme can only undergo a single turnover, which suggests it is a suicide enzyme. It may have additional roles in adaptation to various stress conditions and in DNA damage tolerance .
Acireductone dioxygenase, eukaryotes (ARD_euk)
Type: Family

Acireductone dioxygenase (ARD/MTND, also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase

) is an eukaryotic enzyme that catalyses the formation of formate and 2-keto-4-methylthiobutyrate (KMTB) from 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene). It shows significant homology to the bacterial acireductone dioxygenase (ARD), which is an enzyme in the methionine salvage pathway (MTA cycle) ]. MTCBP-1 is necessary for hepatitis C virus replication in an otherwise non-permissive cell line . MTCBP-1 interacts and inhibits the activity of membrane-type 1 matrix metalloproteinase (MT1-MMP/MMP-14) in promoting tumor cell migration and invasion .

MTCBP-1 contains the cupin sequence motif and belongs to the Cupin superfamily composed of proteins with diverse functions .
Katanin p60 ATPase-containing subunit A-like 2 (Katanin_p60_AL2)
Type: Family

Katanin exists as a heterodimer of a 60kDa AAA-domain-containing catalytic subunit (p60) and an 80kDa targeting and regulatory subunit (p80). Katanin homologues have been identified throughout the animal kingdom and in plants .

Katanin p60 ATPase-containing subunit A-like 2 (KATNAL2) severs microtubules in vitro in an ATP-dependent manner.
Small ribosomal subunit protein uS2, eukaryotic (Ribosomal_uS2_euk)
Type: Family

This entry represents the ribosomal protein of the eukaryotic cytosol that is homologous to uS2 of bacteria. It is designated typically as SA in eukaryotes. The protein is required for the assembly and/or stability of the 40S ribosomal subunit and required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits .

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 .
Glutamyl-tRNA(Gln) amidotransferase subunit F, mitochondrial (GatF)
Type: Family

GatFAB is a trimeric tRNA-dependent amidotransferase (AdT) that allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria . The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). GatF is an essential subunit of the yeast tRNA-dependent amidotransferase .
Small ribosomal subunit protein eS1, eukaryotes (Ribosomal_eS1_euk)
Type: Family

This entry represents the small ribosomal subunit protein eS1 from eukaryotes.

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 .
Lon protease homologue 2, peroxisomal (Lonp2_euk)
Type: Family

This entry represents the peroxisomal lon protease homologue 2 (LON2) from eukaryotes. LON2 is an ATP-dependent serine protease that mediates the selective degradation of misfolded and unassembled polypeptides in the peroxisomal matrix. It is necessary for type 2 peroxisome targeting signal (PTS2)-containing protein processing and facilitates peroxisome matrix protein import .
Inosine triphosphate pyrophosphatase (ITPase)
Type: Family

Inosine triphosphate pyrophosphatase hydrolyses the non-canonical purine nucleotides inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) as well as 2'-deoxy-N-6-hydroxylaminopurine triposphate (dHAPTP) and xanthosine 5'-triphosphate (XTP) to their respective monophosphate derivatives. The enzyme does not distinguish between the deoxy- and ribose forms. It probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions . In yeast, it also hydrolyses 5-bromodeoxyuridine 5'-triphosphate (BrdUTP) .
Lon protease homologue, chloroplastic/mitochondrial (Lonm_euk)
Type: Family

Lon protease is an ATP-dependent serine proteases that mediates the selective degradation of misfolded, unassembled or oxidatively damaged polypeptides as well as certain short-lived regulatory proteins . Proteins in this entry are the eukaryotic homologues of the Lon protease that localise at the mitochondrial matrix. They may also have a chaperone function in the assembly of inner membrane protein complexes. They may participate in the regulation of mitochondrial gene expression and in the maintenance of the integrity of the mitochondrial genome . In plants, they also localise at the chloroplast .
Small ribosomal subunit protein uS2, vertebrates (Ribosomal_uS2_vert)
Type: Family

This entry represents the small ribosomal subunit protein uS2, also known as 40S ribosomal protein SA, from vertebrates (also laminin receptor 1), which is homologous to uS2 of bacteria .

Ribosomal uS2 family in humans includes three members:

Small ribosomal subunits uS2 (also known as RPSA).

Small ribosomal subunits uS2B (also known as RPSA2).

Small ribosomal subunits uS2m in mitochondria (also known as MRPS2).

Ribosomal protein SA (RPSA), previously named 37 kDa laminin receptor precursor/67 kDa laminin receptor (LRP/LR), has been characterised as a multifunctional protein that plays multiple roles in different pathological processes .

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 .
Probable bifunctional methylthioribulose-1-phosphate dehydratase/enolase-phosphatase E1 (MtnB_viridiplantae)
Type: Family

Proteins in this family are probable bifunctional methylthioribulose-1-phosphate dehydratase/enolase-phosphatase E1 from plants. They share protein sequence similarity to both

and

.
7,8-dihydroneopterin aldolase, MptD (DHN_aldolase_MptD)
Type: Family

This family of archaeal 7,8-dihydroneopterin aldolase (also known as dihydroneopterin aldolase) catalyses the conversion of 7,8-dihydroneopterin (H2Neo) to 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP) . 6-HMDP is the precursor of the pterin containing moiety of the essential C1-carriers tetrahydrofolate and tetrahydromethanopterin.
Adenylosuccinate synthetase isozyme 1, chordates (AdSS_1_vert)
Type: Family

This entry represents the adenylosuccinate synthetase isozyme 1 (AdSS1) (

) from vertebrates. It is a component of the purine nucleotide cycle (PNC), which interconverts IMP and AMP to regulate the nucleotide levels in various tissues, and which contributes to glycolysis and ammoniagenesis. It catalyses the first committed step in the biosynthesis of AMP from IMP .
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, MptE (HMPDK_MptE)
Type: Family

This archaeal family of 6-hydroxymethylpterin diphosphokinase (HMDPK), known as MptE, catalyse the formation of 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP) from 6-HMD and ATP . 6-HMDP is the precursor of the pterin containing moiety of the essential C1-carriers tetrahydrofolate and tetrahydromethanopterin.
Enolase-phosphatase E1, eukaryotes (ENOPH1_eukaryotes)
Type: Family

This entry represents the enolase-phosphatase E1 (ENOPH1, also known as MASA) from eukaryotes. ENOPH1 is a bifunctional enzyme that promotes the conversion of 2,3-diketo-5-methylthio-1-phosphopentane to 1,2-dihydroxy-3-keto-5-methylthiopentene anion (an aci-reductone) in the methionine salvage pathway. Besides its function as a phosphatase, it possesses enolase activity that cannot be classified as typical enzymatic enolisation . It's structure has been resolved .
Eukaryotic translation initiation factor 3 subunit A (EIF3A)
Type: Family

Eukaryotic translation initiation factor 3 subunit A is a component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. However, the subunit is not required for the general function of eIF3 in translation initiation . It may play a role in regulating translation of a subset of mRNAs and in regulating cell cycle progression and cell proliferation .
RNA-splicing ligase RtcB homologue, eukaryotic (RtcB_euk)
Type: Family

RctB is a tRNA-splicing ligase from bacteria . RctB homologues in eukaryotes represent the catalytic subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. RctB may act as a RNA ligase with broad substrate specificity, and may function toward other RNAs .
Methylthioribulose-1-phosphate dehydratase, eukaryotes (Salvage_MtnB_euk)
Type: Family

Methylthioribulose-1-phosphate dehydratase catalyses the dehydration of methylthioribulose-1-phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P). It functions in the methionine salvage pathway.
Eukaryotic translation initiation factor 3 subunit C (EIF3C)
Type: Family

Eukaryotic translation initiation factor 3 subunit C (EIF3C) is a component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. EIF3C appears to be important for eIF3 activity . Its N-terminal domain mediates eIF3 binding to eIF1 and eIF5 , and its C-terminal PCI domain forms an important intermolecular bridge between eIF3 and the 40S ribosome .
Deoxyhypusine hydroxylase (Deoxyhypusine_hydroxylase)
Type: Family

Deoxyhypusine hydroxylase (

) catalyses the hydroxylation of the N(6)-(4-aminobutyl)-L-lysine intermediate to form hypusine, an essential post-translational modification only found in mature eIF-5A factor . In Drosophila melanogaster, it is essential for organismal viability and plays a role in a wide number of important processes such as cell growth and proliferation, and regulates induction of autophagy and protein synthesis .
Translation factor GUF1 homologue, organellar chromatophore (GUFP)
Type: Family

Elongation factor 4, also known as ribosomal back-translocase LepA, is present in bacteria and mitochondria, and is required for accurate and efficient protein synthesis under certain stress conditions . The yeast counterpart of LepA is known as GUF1 . GUF1 promotes protein synthesis and acts as a fidelity factor of the translation reaction, by catalysing a one-codon backward translocation of tRNAs on improperly translocated ribosomes.

This entry represents translation factor GUF1 homologues from plants and cyanobacteria (chloroplastic and from organellar chromatophores).
Kynurenine formamidase, vertebrates/fungi-type (KFase_ver/fungi-typ)
Type: Family

Kynurenine formamidase (

) catalyses the hydrolysis of N-formyl-L-kynurenine to L-kynurenine, the second step in the kynurenine pathway of tryptophan degradation. It is required for elimination of toxic metabolites .
Structure-specific endonuclease subunit Slx1 (Slx1)
Type: Family

Slx1 is a catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. It has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA .
U6 snRNA phosphodiesterase 1 (Usb1)
Type: Family

Proteins in this family are phosphodiesterases responsible for trimming the poly (U) tract of the last nucleotides in the pre-U6 snRNA molecule, leading to the formation of mature U6 snRNA .

In Saccharomyces cerevisiae, Usb1 is an essential protein that localises to the nucleus and mitochondria . Usb1 overexpression can compensate for specific respiratory defects of an oxa1 yeast mutant .

In humans, Usb1 is localised to the nucleus and is involved in the 2',3'-cyclic phosphate formation at the 3' end of U6 snRNA . The human protein has been shown to degrade both oligo(U) and oligo(A) tails at the 3' end of U6 snRNA . Its crystal structure has been solved and shows a globular α-β-type architecture . Mutation in Usb1 is linked to poikiloderma with neutropenia (PN), a genodermatosis characterised by poikiloderma, pachyonychia and chronic neutropenia .
Probable alanine--tRNA ligase, plants (Ala_tRNA_synth_plant)
Type: Family

Alanine-tRNA ligase catalyses the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). It also edits incorrectly charged tRNA(Ala) via its editing domain.

This entry consists of probable alanine-tRNA ligases from plants.