SII-SWORD/CoKE huggingface dataset:
Small ribosomal subunit protein uS2, archaeal (Ribosomal_uS2_arc)
Type: Family

This entry represents the archaeal ribosomal protein uS2 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 .
Dihydroorotate dehydrogenase electron transfer subunit (Dihydroorotate_DHASE_ETsu)
Type: Family

Dihydroorotate dehydrogenase (

) (DHOdehase) catalyzes the fourth step in the
de novo
biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria .

This entry represents the electron transfer subunit of dihydroorotate dehydrogenase B (NAD(+)) .
Crotonobetaine/carnitine-CoA ligase CaiC (CaiC)
Type: Family

Many enterobacteria are able to convert carnitine, via crotonobetaine, to gamma-butyrobetaine in the presence of carbon and nitrogen sources under anaerobic conditions . In Escherichia coli the enzymes involved in this pathway are encoded by the caiTABCDE operon . The adjacent but divergent fixABCD operon also appears to be necessary for carnintine meatbolism . The Fix proteins are homologous to proteins found in known electron transport pathways.

One function of CaiC may be to catalyse the transfer of CoA to carnitine, generating the initial carnitinyl-CoA needed for the CaiB reaction cycle . The enzyme also possesses betaine:CoA ligase activity, and is involved in the synthesis of betainyl-CoAs .
Methionine-tRNA synthetase, type 2 (Met-tRNA_synth_2)
Type: Family

Methionine-tRNA ligase (

) is an alpha 2 dimer. In some species (archaea, eubacteria and eukaryotes) a coding sequence, similar to the C-terminal end of MetRS, is present as an independent gene which is a tRNA binding domain as a dimer. In eubacteria, MetRS can also be split in two sub-classes corresponding to the presence of one or two CXXC domains specific to zinc binding. The crystal structures of a number of methionine-tRNA ligases are known .

This entry represents type 2 methionine-tRNA synthetase from eubacteria. Subfamily 2a links one zinc ion whereas subfamily 2b does not .
Methionine-tRNA ligase, type 1 (Met-tRNA_ligase_1)
Type: Family

Methionine-tRNA ligase (

) is an alpha 2 dimer. In some species (archaea, eubacteria and eukaryotes) a coding sequence, similar to the C-terminal end of MetRS, is present as an independent gene which is a tRNA binding domain as a dimer. In eubacteria, MetRS can also be split in two sub-classes corresponding to the presence of one or two CXXC domains specific to zinc binding. The crystal structures of a number of methionine-tRNA ligases are known .

This entry represents type 1 methionine-tRNA ligase, found in eubacteria, archaea and eukaryotes.
Transcription elongation factor GreA/GreB family (Tscrpt_elong_fac_GreA/B_fam)
Type: Family

Bacterial proteins GreA and GreB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as GreA or GreB, allows the resumption of elongation from the new 3' terminus . Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome . GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS.

This entry represents the transcription elongation factor GreA/GreB family. In addition to GreA and GreB, it also includes regulator of nucleoside diphosphate kinase, which is an RNA polymerase-interacting protein that may act as an anti-Gre factor .
RNA-binding family, YbxF-like (RNA_bf_YbxF-like)
Type: Family

This entry represents the YbxF-like (also known as ribosomal eL8 or L7Ae-like) family found in selected Gram-positive bacteria .

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 .
Electron transfer flavoprotein FixB subunit (FixB)
Type: Family

Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, "housekeeping" ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II) .

ETFs are heterodimeric proteins composed of an alpha and beta subunit, and contain an FAD cofactor and AMP . ETF consists of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit. Domains I and III share an almost identical α-β-α sandwich fold, while domain II forms an α-β-α sandwich similar to that of bacterial flavodoxins. FAD is bound in a cleft between domains II and III, while domain III binds the AMP molecule. Interactions between domains I and III stabilise the protein, forming a shallow bowl where domain II resides. The alpha subunit of both Group I and Group II ETFs is composed of domains I and II.

Many enterobacteria are able to convert carnitine, via crotonobetaine, to gamma-butyrobetaine in the presence of carbon and nitrogen sources under anaerobic conditions . In Escherichia coli the enzymes involved in this pathway are encoded by the caiTABCDE operon . The adjacent but divergent fixABCD operon also appears to be necessary for carnintine meatbolism . The Fix proteins are homologous to proteins found in known electron transport pathways.

This entry represents the predicted electron transfer protein alpha subunit FixB, which is necessary for anaerobic carnitine reduction. FixB may be involved in transferring reductant to the CaiA protein.
Electron transfer flavoprotein, FixA subunit (FixA)
Type: Family

Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, "housekeeping" ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II) .

ETFs are heterodimeric proteins composed of an alpha and beta subunit, and contain an FAD cofactor and AMP . ETF consists of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit. Domains I and III share an almost identical α-β-α sandwich fold, while domain II forms an α-β-α sandwich similar to that of bacterial flavodoxins. FAD is bound in a cleft between domains II and III, while domain III binds the AMP molecule. Interactions between domains I and III stabilise the protein, forming a shallow bowl where domain II resides. The alpha subunit of both Group I and Group II ETFs is composed of domains I and II.

Many enterobacteria are able to convert carnitine, via crotonobetaine, to gamma-butyrobetaine in the presence of carbon and nitrogen sources under anaerobic conditions . In Escherichia coli the enzymes involved in this pathway are encoded by the caiTABCDE operon . The adjacent but divergent fixABCD operon also appears to be necessary for carnintine meatbolism . The Fix proteins are homologous to proteins found in known electron transport pathways.

This entry represents the predicted electron transfer protein beta subunit FixA, which is necessary for anaerobic carnitine reduction. FixA may be involved in transferring reductant to the CaiA protein.
DNA-directed RNA polymerase subunit Rpo12 (Rpo12)
Type: Family

DNA-directed RNA polymerases, also known as DNA-dependent RNA polymerases, are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. Eukaryotes have three different DNA-directed RNA polymerases (RNAPs), Pol I, II, and III, whereas Archaea and Bacteria have single enzymes.

RNAPs are multisubunit enzymes. Archaeal RNAP is closely related to eukaryotic RNAP II , which consists of 12 subunits. Archaeal RNAP has an additional subunit, Rpo13, with no orthologue in the eukaryotic enzyme .

This entry represents the archaeal RNA polymerase subunit P, also known as Rpo12 following the eukaryotic nomenclature . Archaeal subunit P is the homologue of eukaryotic subunit Rbp12 .
Riboflavin kinase domain superfamily (Riboflavin_kinase_dom_sf)
Type: Homologous_superfamily

Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (

), which converts it into FMN, and FAD synthetase (

), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme , the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family . The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases .

This entry represents riboflavin kinase, which occurs as part of a bifunctional enzyme or a stand-alone enzyme.
Tetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H (MeTrfase_MtrH/MtxH)
Type: Family

In archaea the enzyme tetrahydromethanopterin S-methyltransferase is composed of eight subunits, MtrA-H. The enzyme is a membrane- associated enzyme complex which catalyzes an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide . Subunit MtrH catalyzes the methylation reaction and was shown to exhibit methyltetrahydromethanopterin:cob(I)alamin methyltransferase activity .

CH3-H4MPT + cob(I)alamin -->H4MPT + CH3-cob(III)alamin (H4MPT = tetrahydromethanopterin)

Methyltransferase MtxH from the archaea Methanosarcina may be part of a complex composed of 3 subunits; MtxA, MtxH and MtxX .

This entry also includes methylcorrinoid:tetrahydrofolate methyltransferase (also known as [methyl-Co(III) glycine betaine-specific corrinoid protein]--tetrahydrofolate methyltransferase) from Desulfitobacterium hafniense, which in vitro catalyses the transfer of a methyl group from methylcobalamin to tetrahydrofolate. In vivo this may permit anaerobic methylotrophic growth using glycine betaine .
Riboflavin kinase (Riboflavin_kinase)
Type: Family

Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (

), which converts it into FMN, and FAD synthetase (

), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme , the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family . The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases .

This entry represents riboflavin kinase, which occurs as part of a bifunctional enzyme or a stand-alone enzyme.
Riboflavin kinase, archaeal (Riboflavin_kinase_archaeal)
Type: Family

Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase, which converts it into FMN, and FAD synthetase, which adenylates FMN to FAD. Bacteria utilize a single bifunctional enzyme containing the ATP-dependent riboflavin kinase and the FMN adenylyltransferase domains. In contrast, two individual and structurally distinct enzymes, cytidine triphosphate (CTP)-dependent riboflavin kinase (RibK) and FAD synthetase (RibL), catalyze the last two steps of the pathway in archaea .

This entry represents RibK.
Cytochrome c oxidase assembly protein CtaG/Cox11, domain superfamily (CtaG/Cox11_dom_sf)
Type: Homologous_superfamily

Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein. In eukaryotes it is an integral protein of the mitochondrial inner membrane. Cox11 is essential for the insertion of Cu(I) ions to form the CuB site. This is essential for the stability of other structures in subunit I, for example haems a and a3, and the magnesium/manganese centre. Cox11 is probably only required in sub-stoichiometric amounts relative to the structural units . The C-terminal region of the protein is known to form a dimer. Each monomer coordinates one Cu(I) ion via three conserved cysteine residues (111, 208 and 210) in Saccharomyces cerevisiae (

). Met 224 is also thought to play a role in copper transfer or stabilising the copper site .

The copper binding motif is composed of two highly conserved cysteines and is located on one side of a β-barrel structure .
Uncharacterised protein family MJ0810 (Uncharacterised_MJ0810)
Type: Family

This entry contains a group of prokaryotic proteins that share protein sequence similarity to eukaryotic Nuclear protein AMMECR1, including Protein PH0010 from Pyrococcus horikoshii. PH0010 consists of two distinct domains of different
sizes: the large domain, which contains both the N- and C-terminal regions, consists of five α-helices and five β-strands that form an antiparallel β-sheet; the small domain consists of four α-helices and three β-strands that also form an antiparallel β-sheet [

,

].
AMMECR1 (AMMECR1)
Type: Family

Nuclear protein AMMECR1, presently a protein of unknown function, is encoded by one of the genes affected by an X-linked deletion that causes the association of Alport syndrome, midface hypoplasia, intellectual disability and elliptocytosis in humans . Homologues appear in species ranging from bacteria and archaea to eukaryotes, including Protein PH0010 from Pyrococcus horikoshii . The high level of conservation of the AMMECR1 domain points to a basic cellular function, potentially in either the transcription, replication, repair or translation machinery .
Exosome complex component Rrp4 (Rrp4)
Type: Family

The archaeal exosome is a protein complex involved in the degradation and the posttranscriptional tailing of RNA . Rrp4 is a structural component of the exosome that confers poly(A) specificity .
Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) CbiT (CbiT)
Type: Family

CbiT is a bifunctional enzyme that catalyses two methylations (at C-5 and C-15) in precorrin-6Y, as well as the decarboxylation of the acetate side chain located in ring C, in order to generate precorrin-8X. It participates in the biosynthesis of vitamin B12 . In the anaerobic pathway, two enzymes are required to produce precorrin-8X: CbiE and CbiT, which can be fused as CbiET (sometimes called CobL) . In the aerobic pathway, the enzyme is a fusion of CbiE and CbiT which is refered to as CobL . CbiT is thought to catalyse one of the methylation reactions .

Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .
Peptidyl-tRNA hydrolase II domain superfamily (Pep_tRNA_hydro_II_dom_sf)
Type: Homologous_superfamily

Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation .

This superfamily represents the structural domain found in these t-RNA hydrolases and which form dimers .
Adenylate kinase AdkA (Adenylate_kinase_AdkA)
Type: Family

AdkA belongs to the archaeal adenylate kinase family . It catalyses the interconversion of adenine nucleotides.
Pyridoxine/pyridoxal/pyridoxamine kinase (PdxK)
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 .

This entry represents pyridoxal kinase PdxK (

), which acts as a pyridoxine (PN)/ pyridoxal (PL)/ pyridoxamine (PM) kinase. PdxK is required for the synthesis of pyridoxal-5-phosphate from vitamin B6 . Its structure has been revealed .
Uncharacterised protein family UPF0312/YceI (UPF0312/YceI)
Type: Family

This entry represents the uncharacterised protein family UPF0312 and the lipid-binding protein YceI from Escherichia coli and its homologues.
Uncharacterised protein family ViaA (Uncharacterised_ViaA)
Type: Family

This entry contains ViaA (VWA domain protein interacting with AAA ATPase) proteins. Their function is unknown.
Uncharacterised protein family Ves (Uncharacterised_Ves)
Type: Family

Proteins of the Ves family have no known function. Ves is induced by various environmental stresses, including low temperature, osmotic shock and oxygen. Expression is induced more than 10 fold by reducing temperature from 37 to 25 degrees Celsius .
Uncharacterised protein family SprT (Uncharacterised_SprT)
Type: Family

The proteins in this entry have no known function and belong to the SprT family.
Transcription initiation factor TFIIB, archaea (TFIIB_arc)
Type: Family

Transcription initiation factor IIB stabilises the TBP (TATA-binding protein) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB).