SII-SWORD/CoKE huggingface dataset:
Rhomboid protease GlpG (Rhomboid_protease_GlpG)
Type: Family

This entry consists of rhomboid protease GlpG and its homologues without the conserved peptidase active sites.

GlpG in E. coli is a rhomboid family intramembrane serine protease that has been extensively characterised as a proxy for rhomboid family proteases in animals. It efficiently cleaves eukaryote-derived model substrates. This multiple membrane-spanning protein excludes inappropriate substrates from access to its cleavage site, and shows activity against truncated versions, but not full-length versions, of the E. coli multidrug transporter MdfA. This finding suggests a housekeeping function in removing faulty proteins. In contrast, several eukaryotic rhomboid family proteases release peptide hormones for signaling functions, and the Shewanella and Vibrio protein rhombosortase appears to be part of a protein-sorting system, cleaving a C-terminal anchoring helix domain .

The tertiary structure from the GlpG protein from E. coli has been determined . The GlpG protein six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.
NADPH dehydrogenase, bacteria (NADPH_DH_bac)
Type: Family

This NADPH dehydrogenase catalyzes the reduction of the double bond of an array of alpha, beta-unsaturated aldehydes and ketones. It also reduces the nitro group of nitroester and nitroaromatic compounds and it could have a role in detoxification processes.

This entry includes a subgroup of NADPH dehydrogenases mostly from Bacillales.
Murein transglycosylase-C (Murein_transglycosylaseC)
Type: Family

Membrane-bound lytic murein transglycosylase C or murein hydrolase C is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division.
2,3-bisphosphoglycerate-independent phosphoglycerate mutase, prokaryotes (ApgAM_prokaryotes)
Type: Family

This family represents 2,3-bisphosphoglycerate-independent phosphoglycerate mutase from baceria and archaea. 2,3-bisphosphoglycerate-independent phosphoglycerate mutase is a metalloenzyme found particularly in archaea and some eubacteria. It is responsble for the interconversion of 2-phosphoglycerate and 3-phosphoglycerate . It is distantly related to the iPGAM (

) characteristic of plants and many eubacteria. The common active site and metal-binding residues of the phosphatase domain are easily identified, but the putative phosphotransferase domain is highly diverged. These proteins are unrelated to the cofactor-dependent PGAM. Activity has been demonstrated for proteins from Methanocaldococcus jannaschii (Methanococcus jannaschii) , Pyrococcus furiosus , and Sulfolobus solfataricus . These proteins were initially misidentified as phosphonopyruvate decarboxylase.
Phosphoglucosamine mutase, archaeal (GlmM_arc)
Type: Family

The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (

) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (

;

) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate . Both PNGM (

) and PAGM (

) are involved in the biosynthesis of UDP-N-acetylglucosamine .

This entry represents the archaeal phosphoglucosamine mutase, GimM. The enzyme converts glucosamine-6-phosphate to glucosamine-1-phosphate as part of the pathway toward UDP-N-acetylglucosamine for peptidoglycan and lipopolysaccharides .
NAD-dependent malic enzyme, proteobacteria (NAD_malic_enz_proteobac)
Type: Family

Proteobacteria NAD-dependent malic enzymes use divalent metal cations as cofactor, with a preference for magnesium or manganese .
They are non-competitively inhibited by high concentrations of NAD+ and L-malate, and activated by aspartate .
Altronate oxidoreductase (Altronate_OxRdtase)
Type: Family

This entry represents a family of bacterial altronate (also known as tagaturonate) oxidoreductases. They are responsible for the NAD-dependent reduction of D-altronate.
Large ribosomal subunit protein uL1, archaea (Ribosomal_uL1_arc)
Type: Family

This entry represents ribosomal uL1 from the archaea; it binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and it is involved in E site tRNA release .

Ribosomal protein uL1 (also known as L1) 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). In
Escherichia coli
, uL1 is known to bind to the 23S rRNA .

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 .
Tyrosine recombinase XerS (Recomb_XerS)
Type: Family

This entry represents the site-specific tyrosine recombinase XerS, which is part of the broader 'phage' integrase family. It acts by catalyzing the cutting and rejoining of recombining DNA molecules. It is essential for converting dimers of the bacterial chromosome into monomers to permit their segregation at cell division .
ATPase RavA (ATPase_RavA)
Type: Family

ATPase RavA or regulatory ATPase variant A functions as an ATPase. It may play a role in metal insertion (metal-chelatase) or as a chaperone. RavA forms a complex with CadA, which represents a possible means of regulating RavA activity in response to acid stress conditions. This interaction results in an increase in RavA ATPase activity. Five RavA oligomers interact with two CadA decamers .
Large ribosomal subunit protein uL2, archaeal-eukaryota type (Ribosomal_uL2_arc_euk)
Type: Family

Ribosomal protein uL2 is one of the proteins from the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups:

Eubacterial uL2.

Algal and plant chloroplast uL2.

Cyanelle uL2.

Archaebacterial uL2.

Plant uL2.

Slime mold uL2.

Marchantia polymorpha mitochondrial uL2.

Paramecium tetraurelia mitochondrial uL2.

Fission yeast K5, K37 and KD4.

Yeast YL6.

Vertebrate uL2 (old name L8).

This entry represents the ribosomal protein uL2 from archaea. All members belong to the uL2 family.

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 .
Large ribosomal subunit protein uL1, conserved site (Ribosomal_uL1_CS)
Type: Conserved_site

Ribosomal protein uL1 is the largest protein from the large ribosomal subunit. In Escherichia coli, uL1 is known to bind to the 23S rRNA

This entry represents the best conserved region located in the central section of these proteins, at the end of an α-helix thought to be involved in RNA-binding.

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 .
Ribosomal protein uL1-like (Ribosomal_uL1-like)
Type: Homologous_superfamily

This entry represents a structural domain common to several uL1 ribosomal proteins, and related proteins. It consists of one α/β subdomain interrupted by another α/β subdomain.

Ribosomal protein uL1 is the largest protein from the large ribosomal subunit. In Escherichia coli, uL1 is known to bind to the 23S rRNA :
Small ribosomal subunit protein uS14, archaea (Ribosomal_uS14_arc)
Type: Family

The entry includes the small ribosomal subunit protein uS14 from archaea, which belong to the zinc-binding subfamily of ribosomal protein uS14. They bind 1 zinc ion per subunit and bind to the 16S rRNA. uS14 is required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.

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 .
UbiD decarboxylyase, bacteria (UbiD_bacteria)
Type: Family

3-octaprenyl-4-hydroxybenzoate carboxy-lyase (also known as UbiD) catalyses the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol. It is involved in ubiquinone biosynthesis .
Tyrosine-tRNA ligase, type 4 (Tyr-tRNA-ligase_4)
Type: Family

The group of proteins in this entry are tyrosine-tRNA ligases from archaea, and they belong to tyrosine-tRNA ligases type 4.

Tyrosine-tRNA ligases (TyrRS; also known as Tyrosyl-tRNA synthetases) (

) are widely distributed, being found in archaea, bacteria and eukaryotes. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the class I characteristic 'HIGH' and 'KMSKS' motifs, which are involved in ATP binding. Studies have shown that the 'KMSKS' motif plays a role in the initial binding of tRNA(Tyr) to tyrosine-tRNA ligase .

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .

The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases .
Uncharacterised protein family UPF0761, bacterial (UPF0761_bac)
Type: Family

This entry represents bacterial members of the uncharacterised protein family UPF0761. It includes the E. coli gene product of yihY, and was previously thought to be a family of tRNA-processing ribonuclease BN proteins . This has been shown to be incorrect .
Purine ribonucleoside efflux pump, NepI (MFS_NepI)
Type: Family

Among the different families of transporter, only two occur ubiquitously in all classifications of organisms. These are the ATP-Binding Cassette (ABC) superfamily and the Major Facilitator Superfamily (MFS). The MFS transporters are single-polypeptide secondary carriers capable only of transporting small solutes in response to chemiosmotic ion gradients .

This entry represents the nucleoside efflux permease-inosine (NepI) subfamily of the MSF superfamily. These proteins are nucleoside efflux pumps and are involved in the efflux of purine ribonucleosides, such as guanosine, adenosine and especially inosine .
Tyrosine-tRNA ligase, type 3 (Tyr-tRNA-ligase_3)
Type: Family

The group of proteins in this entry are tyrosine-tRNA ligases from archaea, and they belong to tyrosine-tRNA ligases type 3.

Tyrosine-tRNA ligases (TyrRS; also known as Tyrosyl-tRNA synthetases) (

) are widely distributed, being found in archaea, bacteria and eukaryotes. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the class I characteristic 'HIGH' and 'KMSKS' motifs, which are involved in ATP binding. Studies have shown that the 'KMSKS' motif plays a role in the initial binding of tRNA(Tyr) to tyrosine-tRNA ligase .

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .

The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases .
Pyridoxal kinase PdxY (Pyridoxal_kinase_PdxY)
Type: Family

Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .

PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the ε-amino group of an active site lysine residue on the enzyme. The α-amino group of the substrate displaces the lysine ε-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic .

Pyridoxal kinase PdxY (Escherichia coli pyridoxal kinase 2 or ePL kinase 2) phosphorylates B6 vitamers. PdxY acts in the salvage pathway of pyridoxal 5'-phosphate biosynthesis . It has been shown to have some pyridoxal (PL) kinase activity, but at a greatly reduced level compared to the enzyme expressed by the pdxK gene (ePL kinase 1) .