SII-SWORD/CoKE huggingface dataset:
Vitellinogen, beta-sheet shell (Vitellinogen_b-sht_shell)
Type: Domain

This entry represents the β-sheet shell domain found in vitellinogen, which generally corresponds to the lipovitellin-2 peptide product. This domain consists of several large open β-sheets . It is often found C-terminal to

and

.

Vitellinogen precursors provide the major egg yolk proteins that are a source of nutrients during early development of oviparous vertebrates and invertebrates. Vitellinogen precursors are multi-domain apolipoproteins that are cleaved into distinct yolk proteins. Different vitellinogen precursors exist, which are composed of variable combinations of yolk protein components; however, the cleavage sites are conserved .

In vertebrates, a complete vitellinogen is composed of an N-terminal signal peptide for export, followed by four regions that can be cleaved into yolk proteins: lipovitellin-1, phosvitin, lipovitellin-2, and a von Willebrand factor type D domain (YGP40). Vitellinogens are post-translationally glycosylated and phosphorylated in the endoplasmic reticulum and Golgi complex of hepatocytes, before being secreted into the circulatory system to be taken up by oocytes. In the ovary, vitellinogens bind to specific Vtgr receptors on oocyte membranes to become internalised by endocytosis, where they are cleaved into yolk proteins by cathepsin D. YGP40 is released into the yolk plasma before or during compartmentation of lipovitellin-phosvitin complex into the yolk granule.

The different yolk proteins have distinct roles. Phosvitins are important in sequestering calcium, iron and other cations for the developing embryo. Phosvitins are one of the most phosphorylated (10%) proteins in nature, the high concentration of phosphate groups providing efficient metal-binding sites in clusters . Lipovitellins are involved in lipid and metal storage, and contain a heterogeneous mixture of about 16% (w/w) noncovalently bound lipid, most being phospholipid. Lipovitellin-1 contains two chains, LV1N and LV1C .
Methylene-tetrahydromethanopterin dehydrogenase, N-terminal (Methyl-teptahyd_DH_N)
Type: Domain

Prokaryotic methylene-tetrahydromethanopterin dehydrogenase catalyses the dehydrogenation of methylene-tetrahydromethanopterin during growth on one-carbon compounds such as methanol. It can also catalyse the reversible dehydrogenation of methylene-tetrahydrofolate, though at much lower efficiency . The pterin domain of this protein is composed of two α-β segments found at the N- and C-terminal ends of the polypeptide respectivly. This entry represents the N-terminal segment of the pterin domain, with a core comprising three α/β/α layers in which each sheet contains four strands.
Syntaxin 6/10/61, N-terminal (Syntaxin-6/10/61_N)
Type: Domain

This domain is found in the N-terminal of various SNARE proteins, including Syntaxin 6/10/61, adopt a structure consisting of an antiparallel three-helix bundle. Its exact function has not been determined, though it is known that it regulates the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport .
4-alpha-glucanotransferase, C-terminal (4-alpha-glucanotransf_C)
Type: Domain

Members of this entry, which are predominantly found in prokaryotic 4-alpha-glucanotransferase, adopt a structure composed of six antiparallel β-strands, four of which form a β-sheet and another two form a type I, β-hairpin. The role of this family of domains, has not, as yet, been defined .
Prolyl-tRNA synthetase, class II, C-terminal, archaeal-type (Pro-tRNA_synth_II_arc)
Type: Domain

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 .

This domain is found predominantly found in prolyl-tRNA synthetases from archaeal Methanococci species. It contains a zinc binding site, and adopts a structure consisting of α helices and antiparallel β sheets arranged in 2 layers, in a β-α-β-α-β motif .
Bacterial purine repressor, N-terminal (PuR_N)
Type: Domain

The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA .
Domain of unknown function DUF1947 (DUF1947)
Type: Domain

Members of this entry are a set of hypothetical archaeal proteins. Their exact function has not, as yet, been defined.
Protein phosphatase 4 core regulatory subunit R2 (PPP4R2)
Type: Family

Protein phosphatase 4 core regulatory subunit R2 (PPP4R2), also known as Psy4 in budding yeast, is the regulatory subunit of the histone H2A phosphatase complex. The histone H2A phosphatase complex dephosphorylates H2AS128ph (gamma-H2A) that has been displaced from sites of DNA lesions in the double-stranded DNA break repair process. Dephosphorylation of Psy4 is necessary for efficient recovery from the DNA damage checkpoint .
Protein of unknown function DUF1948 (DUF1948)
Type: Family

Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central α-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined .
Uncharacterised domain UPF0029, Impact, C-terminal (UPF0029_Impact_C)
Type: Domain

Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a β-α-β-β-α-β arrangement .
Protein RDM1, plant (RDM1_plant)
Type: Family

This family includes protein RDM1 from Arabidopsis, which is a a small protein that binds single-stranded methyl DNA, and associates and co-localises with RNA polymerase II, AGO4 and DRM2 in the nucleus. RDM1 is a component of the RNA-directed DNA methylation effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation .
Protein of unknown function DUF1951 (DUF1951)
Type: Family

This entry consists of Mycoplasma hypothetical proteins that adopt a multi-helical structure containing a buried central helix. Their function has not been determined yet.
Molybdopterin cofactor biosynthesis MoaD-related, C-terminal (Mopterin_CF_MoaD-rel_C)
Type: Domain

In Escherichia coli, the MoaD protein plays a central role in the conversion of precursor Z to molybdopterin (MPT) during molybdenum cofactor biosynthesis. Proteins are found in Thermus thermophilus, including threonine synthase (

), which catalyses the conversion of O-phospho-L-homoserine to L-threonine and phosphate.

MoaD-related proteins have an N-terminal MoaD domain, with a fold similar to that of ubiquitin, and contain a highly conserved C-terminal Gly-Gly motif, which in its active form contains a transferrable sulphur in the form of a thiocarboxylate group . This entry represents the domain found at the C terminus, which consists of a TBP-like fold of β/α/β(4)/α.
Cysteinyl-tRNA synthetase, class Ia, DALR (Cys-tRNA-synt_Ia_DALR)
Type: Domain

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 .

This DALR domain is found in cysteinyl-tRNA-synthetases .
CD4, extracellular (CD4-extracel)
Type: Domain

This domain adopts an immunoglobulin-like β-sandwich with seven strands in 2 β sheets, in a Greek key topology. It is predominantly found in the extracellular portion of CD4 proteins, where it enables interaction with major histocompatibility complex class II antigens .
Actin-fragmin kinase, catalytic domain (Actin-fragmin_kin_cat_dom)
Type: Domain

This domain assumes a secondary structure consisting of eight β strands and 11 α-helices, organised in two lobes. It is predominantly found in actin-fragmin kinase. It is the catalytic domain that mediates the phosphorylation of actin .

An atypical actin-fragmin kinase domain is also found at the N terminus of dual-specificity phosphatases such as propyzamide-hypersensitive 1 (PHS1) .
Cholecystokinin A receptor, N-terminal (CholecystokininA_recpt_N)
Type: Domain

This entry represents the extracellular N-terminal domain of the cholecystokinin A receptor. This domain adopts a tertiary structure consisting of a few helical turns and a disulphide-cross linked loop. It is required for interaction of the cholecystokinin A receptor with its corresponding hormonal ligand .
Restriction endonuclease, type II, AvaI/BsoBI (Restrct_endonuc_II_AvaI/BsoBI)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry represent AvaI and BsoBI restriction endonucleases, both of which recognise the double-stranded sequence CYCGRG (where Y = T/C, and R = A/G) and cleave after C-1 .
Type-2 restriction enzyme BglII (BglII)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry represents BglII restriction endonucleases, which recognise AGATCT and cleaves after A-1 . BglII adopts a structure consisting of an α/β core containing a six-stranded β-sheet surrounded by five α-helices, two of which are involved in homodimerisation of the endonuclease.
Malto-oligosyltrehalose synthase, C-terminal (Trehalose_TreY_C)
Type: Domain

This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp . Its function has not, as yet, been defined.
Rap1, DNA-binding domain (Rap1_DNA-bd)
Type: Domain

Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site .
DNA beta-glucosyltransferase, bacteriophage (Phage_Bgt)
Type: Family

Members of this family include DNA-modifying enzymes encoded by bacteriophage T4 that catalyses the transfer of glucose (Glc) from uridine diphosphoglucose (UDP-Glc) to 5-hydroxymethylcytosine (5-HMC) in double-stranded DNA . It is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system .
Staphylococcal superantigen-like OB-fold domain (SSL_OB)
Type: Domain

This OB-fold domain folds into a five-stranded β-barrel . Proteins containing this domain are found in various staphylococcal toxins described as staphylococcal superantigen-like (SSL) proteins that are related to the staphylococcal enterotoxins (SEs) or superantigens. These SSL proteins of which 11 have so far been characterised have a typical SE tertiary structure consisting of a distinct oligonucleotide/oligosaccharide binding (OB-fold), this domain, linked to a β-grasp domain, family Stap_Strp_tox_C (

). SSLs do not bind to T-cell receptors or major histocompatibility complex class II molecules and do not stimulate T cells. SSLs target components of innate immunity, such as complement, Fc receptors, and myeloid cells . SSL protein 7 (SSL7) is the best characterised of the SSLs and binds complement factor C5 and IgA with high affinity and inhibits the end stage of complement activation and IgA binding to FcgammaR .
Monellin (Monellin)
Type: Family

Monellin, a protein produced by the West African plant Dioscoreophyllum cumminsii (Serendipity berry), is approximately 70,000 times sweeter than sucrose on a molar basis. The protein adopts an α-β structure, with a cystatin-like fold, where each helix packs against a coiled antiparallel β-sheet .
Signal recognition particle (SRP) receptor alpha subunit, N-terminal (SRX_dom)
Type: Domain

This domain (SRX domain) is found in the signal recognition particle receptor (SR) subunit alpha, also known as Srp101 in budding yeast, which consist of a central six-stranded anti-parallel β-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. The SRX domain of SRalpha can bind SRbeta, and the affinity of GDP bound SRbeta for SRX is several orders of magnitude lower compared to the GTP bound state .

Srp101 is a homologue of the human SRalpha (signal recognition particle receptor alpha subunit), which is part of the SR complex involved in targeting the nascent secretory proteins to the endoplasmic reticulum membrane system. Similar to human SRslpha, Srp101 also forms SR complex with the SRbeta subunit, Srp102 .
RIO2 kinase winged helix domain, N-terminal (RIO2_wHTH_N)
Type: Domain

This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four α helices followed by two β strands and a fifth α helix. The domain confers DNA binding properties to the protein, as per other winged helix domains .
Porin family, mycobacterial-type (Porin_fam_mycobact-type)
Type: Family

MspA is a membrane porin produced by Mycobacteria, allowing hydrophilic nutrients to enter the bacterium. The protein forms a tightly interconnected octamer with eightfold rotation symmetry that resembles a goblet and contains a central channel. Each subunit fold contains a β-sandwich of Ig-like topology and a β-ribbon arm that forms an oligomeric transmembrane barrel . The Mycobacterium smegmatis genome encodes four paralogues, MspA, MspB, MspC and MspD, which are also represented by this entry.
Colicin D immunity protein domain (Colicin_D_immunity_dom)
Type: Domain

Colicin D is a bacteriocin that kills target cells by cleaving tRNA(Arg). Colicin D immunity protein (ImmD) inhibits the bactericidal activity of colicin D by binding to its tRNase catalytic domain .
Protein of unknown function DUF1955 (DUF1955)
Type: Family

Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus. Their exact function has not, as yet, been determined. These proteins fold into a right-handed superhelix assembled from ten, repeated in tandem, α-helices

.
Alpha-L-arabinofuranosidase B, catalytic (A-L-arabinofuranosidase_B_cat)
Type: Domain

This domain, found in fungal alpha-L-arabinofuranosidase B, adopts a β-sandwich fold similar to that of concanavalin A-like lectins/glucanase. The β-sandwich fold consists of two anti-parallel β-sheets with seven and six strands, respectively. In addition, there are four helices outside of the β-strands. The β-sandwich strands are closely packed and curved with a jelly roll topology, creating a small catalytic pocket. The domain catalyses the hydrolysis of alpha-1,2-, alpha-1,3- and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan and L-arabinan .
Yeast killer toxin (Yeast-kill-tox)
Type: Family

Proteins in this family, which are produced by Williopsis fungi, adopt a secondary structure consisting of eight strands in two β sheets, in a Greek-key topology . They are toxic, killing sensitive strains of yeast.