SII-SWORD/CoKE huggingface dataset:
Asp/Glu/hydantoin racemase (Asp/Glu/hydantoin_racemase)
Type: Family

This entry represents a group of related proteins that includes aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase. Two conserved cysteines are present in the sequence of these enzymes. They play a role in catalytic activity by acting as bases in proton abstraction from the substrate .

Aspartate racemase (

) and glutamate racemase (

) are two evolutionary related bacterial enzymes that do not seem to require a cofactor for their activity . Glutamate racemase, which interconverts L-glutamate into D-glutamate, is required for the biosynthesis of peptidoglycan and some peptide-based antibiotics such as gramicidin S. The E.coli L-aspartate/glutamate specific racemase Ygea, which was previously an hypothetical protein, has been shown to have racemase activity for both L-glutamate and L-aspartate with higher preference for L-glutamate .

Hydantoin racemases catalyse the racemization of various 5-substituted hydantoins. The structure of the allantoin racemase from Klebsiella pneumoniae has been solved .
WD40/YVTN repeat-like-containing domain superfamily (WD40/YVTN_repeat-like_dom_sf)
Type: Homologous_superfamily

This superfamily represents a WD40/YVTN repeat-like domain. Both the WD40 and the YVTN repeated motifs consist of about 40 residues, and although they consist of distinct sequences, they do share a similar structure. Structurally, both the WD40 and the YVTN repeated motifs form seven-bladed propellers (although some members can contain eight blades), which consist of seven 4-stranded β-sheets.
Glycine-tRNA ligase, beta subunit (Gly-tRNA-synth_bsu)
Type: Family

This entry represents the beta subunit of glycine-tRNA ligase.

The aminoacyl-tRNA synthetases (

) 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 and are mostly monomeric, while class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet formation, flanked by α-helices , and are mostly dimeric or multimeric. 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 aci, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases.

The 10 class I synthetases are considered to have in common the catalytic domain structure based on the Rossmann fold, which is totally different from the class II catalytic domain structure. The class I synthetases are further divided into three subclasses, a, b and c, according to sequence homology. No conserved structural features for tRNA recognition by class I synthetases have been established.
K homology domain-like, alpha/beta (KH_dom-like_a/b)
Type: Homologous_superfamily

The K homology domain is a common RNA-binding motif present in one or multiple copies in both prokaryotic and eukaryotic regulatory proteins. The KH motifs may act cooperatively to bind RNA in the case of multiple motifs, or independently in the case of single KH motif proteins. Prokaryotic (pKH) and eukaryotic (eKH) KH domains share a KH-motif, but have different topologies. The pKH domain has been found in a number of proteins, including the N-terminal domain of the S3 ribosomal protein , the C-terminal domain of Era GTPase and the two C-terminal domains of the NusA transcription factor . The structure of the pKH domain consists of a two-layer α/β fold in the arrangement α/β(2)/α/β.

This entry represents K homology domains, as well as related domains that share the same 2-layer α/β structure.
PUA-like superfamily (PUA-like_sf)
Type: Homologous_superfamily

This superfamily represents domains with a PUA-like structure, consisting of a pseudo-barrel composed of mixed folded sheets of five strands. This structural motif is found in:

PUA-containing proteins.

The N-terminal of ATP sulphurylases, which contains extra structures, some similar to the PK β-barrel domain .

Several bacterial hypothetical proteins, such as the N-terminal domain of YggJ .

The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found . PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis . The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA . PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases .
Bacteriophage PRD1, P2, C-terminal (Phage_PRD1_P2_C)
Type: Homologous_superfamily

The absorption protein P2 (synonym: receptor-binding protein P2) from the bacteriophage PRD1 is a multi-β-sheet protein whose complicated topology forms an elongated seahorse-shaped molecule with a distinct head, containing a pseudo-β propeller structure with approximate 6-fold symmetry, and a tail (β-sandwich). It is required for the attachment of the phage to the host conjugative DNA transfer complex. This is a poorly understood large transmembrane complex of unknown architecture, with at least 11 different proteins .

This entry represents the pseudo β-propeller region.
Bacteriophage PRD1, P2, N-terminal (Phage_PRD1_P2_N)
Type: Homologous_superfamily

The absorption protein P2 (synonym: receptor-binding protein P2) from the bacteriophage PRD1 is a multi-β-sheet protein whose complicated topology forms an elongated seahorse-shaped molecule with a distinct head, containing a pseudo-β propeller structure with approximate 6-fold symmetry, and a tail (β-sandwich). It is required for the attachment of the phage to the host conjugative DNA transfer complex. This is a poorly understood large transmembrane complex of unknown architecture, with at least 11 different proteins .
Chemokine-binding M3, subdomain 1, viral (Chemokine-bd_M3_sub1_vir)
Type: Homologous_superfamily

This entry represents a β-sandwich domain found in a group of viral chemokine binding proteins. These proteins bind with CC-chemokine MCP-1, acting as cytokine decoy receptors . For example, the murine herpesvirus decoy receptor M3 acts as an immune system saboteur by altering host anti-viral inflammatory repsonses. M3 adopts a structure consisting of two different β-sandwich domains of partial topological similarity to immunoglobulin-like folds.

This entry represents the N-terminal β-sandwich domain.
Chemokine-binding M3, subdomain 2, viral (Chemokine-bd_M3_sub2_vir)
Type: Homologous_superfamily

This entry represents the C-terminal of a β-sandwich domain found in a group of viral chemokine binding proteins. These proteins bind with CC-chemokine MCP-1, acting as cytokine decoy receptors . For example, the murine herpesvirus decoy receptor M3 acts as an immune system saboteur by altering host anti-viral inflammatory repsonses. M3 adopts a structure consisting of two different β-sandwich domains of partial topological similarity to immunoglobulin-like folds.
Methane monooxygenase, gamma chain, domain 1 (Me_mOase_g_dom1)
Type: Homologous_superfamily

Methane monooxygenases (

) catalyse the oxidation of methane to methanol in the presence of oxygen and NADH in methanotrophs. It has a broad specificity, hydroxylating many alkanes, and converting alkenes into the corresponding epoxides. In additional reactions, CO is oxidized to CO2, ammonia is oxidized to hydroxylamine, and some aromatic compounds and cyclic alkanes can also be hydroxylated, although more slowly. In Methylococcus capsulatus there are two forms of the enzyme, a soluble and a membrane-bound type. The soluble form consists of 3 components, A, B and C. Protein A is made up of 3 chains, alpha, beta and gamma.
Methane monooxygenase, gamma chain, domain 2 (Me_mOase_g_dom2)
Type: Homologous_superfamily

Methane monooxygenases (

) catalyse the oxidation of methane to methanol in the presence of oxygen and NADH in methanotrophs. It has a broad specificity, hydroxylating many alkanes, and converting alkenes into the corresponding epoxides. In additional reactions, CO is oxidized to CO2, ammonia is oxidized to hydroxylamine, and some aromatic compounds and cyclic alkanes can also be hydroxylated, although more slowly. In Methylococcus capsulatus there are two forms of the enzyme, a soluble and a membrane-bound type. The soluble form consists of 3 components, A, B and C. Protein A is made up of 3 chains, alpha, beta and gamma.
Bacteriophage RNA-type, capsid (Phage_RNA-type_capsid)
Type: Homologous_superfamily

This entry represents capsid coat proteins from a variety of RNA bacteriophages, including Bacteriophage MS2, Bacteriophage GA, Bacteriophage fr, Bacteriophage Q-beta and Pseudomonas phage PP7. These capsid coat proteins share a similar structure, consisting of a 6-stranded β-sheet followed by two helices. Capsid proteins form the bacteriophage coat that encapsidates the viral RNA. In Bacteriophage MS2, 180 copies of this protein form the virion shell and control two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication .
Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (Lactate_DH/Glyco_Ohase_4_C)
Type: Homologous_superfamily

This entry represents a structural motif found at the C-terminal of lactate dehydrogenase (

)and malate dehydrogenases (

), as well as at the C-terminal of family 4 glycoside hydrolases (

). These domains have an unusual fold consisting of segregated α-helical and β-sheet regions, although they contain predominantly anti-parallel β-sheets .

L-lactate dehydrogenases are metabolic enzymes that catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle.

O-Glycosyl hydrolases

are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Glycoside hydrolase family 4

comprises enzymes with several known activities; 6-phospho-beta-glucosidase (

); 6-phospho-alpha-glucosidase (

); alpha-galactosidase (

).
Penicillin-binding protein, C-terminal domain superfamily (Peniciliin-bd_prot_C_sf)
Type: Homologous_superfamily

This superfamily represents a structural motif found at the C-terminal of penicillin-binding proteins 4 (PBP4) and 5 (PBP5), as well as at the C-terminal of D-Ala-D-Ala carboxypeptidase A, a member of the MEROPS S11 peptidase family (PBP4 and PBP5 also belong to this peptidase family). These domains share a similar structure, consisting of a β-sandwich of six strands in two sheets .

Penicillin-binding proteins are beta-lactam antibiotic-sensitive bacterial enzymes required for the growth and maintenance of the peptidoglycan layer of the bacterial cell wall that protects the cell from osmotic stress. PBP4 functions as a transpeptidase, acting co-operatively with PBP2 in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents .
Potassium transporter Trk1, fungi (Trk1_fungi)
Type: Family

Trk1 (also known as Trk) transporters play a crucial roles in K(+) transport in yeasts and filamentous fungi .
Mu1 membrane penetration protein, domain IV (Mu1_membr_pen_domIV)
Type: Homologous_superfamily

Mu1 is an outer capsid protein that acts as a reoviral penetration agent. Non-enveloped animal reoviruses must enter host cells by membrane penetration that does not involve membrane fusion, as they lack a viral membrane. Reoviruses are activated by proteolytic cleavage in the intestinal lumen, leading to infectious subviral particles. The core of the virus is coated by a layer of mu1 and sigma3 proteins. Proteases strip off sigma3 exposing mu1, which provides the membrane penetration machinery that perforates the membrane. In addition, N-terminal myristoylation of polypeptide Mu1 is required for site-specific cleavage to Mu1C in transfected cells . Mu1 forms a trimer, where the three mu1 molecules are coiled around one another with a right-handed twist. The mu1 chain folds into four distinct domains: three intertwined, predominantly α helical domains and a jelly-roll β-sandwich .

This superfamily represents the jelly-roll β-sandwich domain.
Mu1 membrane penetration protein, domain I (Mu1_membr_pen_domI)
Type: Homologous_superfamily

Mu1 is an outer capsid protein that acts as a reoviral penetration agent. Non-enveloped animal reoviruses must enter host cells by membrane penetration that does not involve membrane fusion, as they lack a viral membrane. Reoviruses are activated by proteolytic cleavage in the intestinal lumen, leading to infectious subviral particles. The core of the virus is coated by a layer of mu1 and sigma3 proteins. Proteases strip off sigma3 exposing mu1, which provides the membrane penetration machinery that perforates the membrane. In addition, N-terminal myristoylation of polypeptide Mu1 is required for site-specific cleavage to Mu1C in transfected cells . Mu1 forms a trimer, where the three mu1 molecules are coiled around one another with a right-handed twist. The mu1 chain folds into four distinct domains: three intertwined, predominantly α helical domains and a jelly-roll β-sandwich .
Mu1 membrane penetration protein, domain II (Mu1_membr_pen_domII)
Type: Homologous_superfamily

Mu1 is an outer capsid protein that acts as a reoviral penetration agent. Non-enveloped animal reoviruses must enter host cells by membrane penetration that does not involve membrane fusion, as they lack a viral membrane. Reoviruses are activated by proteolytic cleavage in the intestinal lumen, leading to infectious subviral particles. The core of the virus is coated by a layer of mu1 and sigma3 proteins. Proteases strip off sigma3 exposing mu1, which provides the membrane penetration machinery that perforates the membrane. In addition, N-terminal myristoylation of polypeptide Mu1 are required for site-specific cleavage to Mu1C in transfected cells . Mu1 forms a trimer, where the three mu1 molecules are coiled around one another with a right-handed twist. The mu1 chain folds into four distinct domains: three intertwined, predominantly α helical domains and a jelly-roll β-sandwich .
Uridylate kinase, bacteria (Uridylate_kinase_bac)
Type: Family

Uridylate kinases (also known as UMP kinases) are key enzymes in the synthesis of nucleoside triphosphates. They catalyse the reversible transfer of the gamma-phosphoryl group from an ATP donor to UMP, yielding UDP, which is the starting point for the synthesis of all other pyrimidine nucleotides. The eukaryotic enzyme has a dual specificity, phosphorylating both UMP and CMP, while the bacterial enzyme is specific to UMP. The bacterial enzyme shows no sequence similarity to the eukaryotic enzyme or other nucleoside monophosphate kinases, but rather appears to be part of the amino acid kinase family. It is dependent on magnesium for activity and is activated by GTP and repressed by UTP . In many bacterial genomes, the gene tends to be located immediately downstream of elongation factor T and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function is found in the archaea and in spirochetes.

Structurally, the bacterial and archaeal proteins are homohexamers centred around a hollow nucleus and organised as a trimer of dimers . Each monomer within the protein forms the amino acid kinase fold and can be divided into an N-terminal region which binds UMP and mediates intersubunit interactions within the dimer, and a C-terminal region which binds ATP and contains a mobile loop covering the active site. Inhibition of enzyme activity by UTP appears to be due to competition for the binding site for UMP, not allosteric inhibition as was previously suspected.

Uridylate kinase PUMPKIN, chloroplastic from Arabidopsis thaliana is essential for retaining photosynthetic activity in chloroplasts as it is required for specific post-transcriptional processes of many plastid transcripts .

This entry represents uridine monophosphate kinase predominantly found in bacteria and plant chloroplasts.
tRNA ligase, phosphodiesterase (tRNA_lig_PDEase)
Type: Domain

This entry represents a phosphodiesterase domain found in tRNA ligases .
tRNA ligase, kinase domain, fungi (tRNA_lig_kin_fungi)
Type: Domain

This entry represents a kinase domain found in fungal tRNA ligases . tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. This domain contains a P-loop motif.
Recombination protein RecR, zinc finger domain (Rcmb_RecR_Znf)
Type: Domain

This conserved site represents the C4-type zinc finger which contains four strictly conserved cysteine residues that coordinates a zinc ion . Mutations in this domain affects bacterial survival suggesting that it plays an important role, likely in DNA binding .

The bacterial protein RecR is an important regulator in the RecFOR homologous recombination pathway during DNA repair . It acts with RecF and RecO forming a complex that facilitates the loading of RecA onto ssDNA . RecR is a zinc metalloprotein consisting of a N-terminal helix-hairpin-helix (HhH) motif, a middle region containing a zinc finger motif and a Toprim domain, and a C-terminal domain comprising a divergent Walker B motif and a C-terminal helix .
P40 nucleoprotein, subdomain 1, Borna disease virus (P40_nucleoprot_sub1_BD-vir)
Type: Homologous_superfamily

This entry represents P40 nucleoproteins from several Borna disease virus (BDV) strains. BDV is an RNA virus that is a member of the Mononegavirales family, which includes such members as Measles virus and Ebola virus sp.. BDV causes an infection of the central nervous system in a wide range of vertebrates, which can progress to an often fatal immune-mediated disease known as Borna disease. Viral nucleoproteins are central to transcription, replication, and packaging of the RNA genome. P40 nucleoprotein from BDV is multi-helical in structure and can be divided into two subdomains, each of which has an α-bundle topology . The nucleoprotein assembles into a planar homotetramer, with the RNA genome either wrapping around the outside of the tetramer or possibly fitting within the charged central channel of the tetramer .

This entry represents one of the two α-bundle subdomains.
P40 nucleoprotein, subdomain 2, Borna disease virus (P40_nucleoprot_sub2_BD-vir)
Type: Homologous_superfamily

This entry represents P40 nucleoproteins from several Borna disease virus (BDV) strains. BDV is an RNA virus that is a member of the Mononegavirales family, which includes such members as Measles virus and Ebola virus sp.. BDV causes an infection of the central nervous system in a wide range of vertebrates, which can progress to an often fatal immune-mediated disease known as Borna disease. Viral nucleoproteins are central to transcription, replication, and packaging of the RNA genome. P40 nucleoprotein from BDV is multi-helical in structure and can be divided into two subdomains, each of which has an α-bundle topology . The nucleoprotein assembles into a planar homotetramer, with the RNA genome either wrapping around the outside of the tetramer or possibly fitting within the charged central channel of the tetramer .

This entry represents one of the two α-bundle subdomains.
Nucleocapsid, Phlebovirus (Nucleocapsid_Phlebovirus)
Type: Family

This family consists of several Phlebovirus nucleocapsid proteins.
Large ribosomal subunit protein eL19, domain 1 (Ribosomal_eL19_dom1)
Type: Homologous_superfamily

This entry represents the N-terminal domain of the large ribosomal subunit protein eL19 found in eukaryotes and archaea . eL19 is part of the large ribosomal subunit, whose structure has been determined in a number of eukaryotic and archaeal species . eL19 is a multi-helical protein consisting of two different 3-helical domains connected by a long, partly helical linker. This superfamily represents an α-helical domain that assumes an orthogonal bundle topology.

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 .