SII-SWORD/CoKE huggingface dataset:
Restriction endonuclease, type II, MspI (Restrct_endonuc_II_MspI)
Type: Family

This entry represents type II restriction endonucleases such as MspI, which recognises the palindromic tetranucleotide sequence 5'-CCGG and cleave between the first and second nucleotides, leaving 2 base 5' overhangs. They fold into an α/β architecture, with a five-stranded mixed β-sheet sandwiched on both sides by α-helices .

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 .
Transcription regulator YbiH, C-terminal (Tscrpt_reg_YbiH_C)
Type: Domain

This entry represents the C-terminal domain found in the hypothetical transcriptional regulator YbiH from bacteria such as Salmonella typhimurium and Escherichia coli. YbiH is a member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. The C-terminal domains of YbiH and TetR share a multi-helical, interlocking structure.
1,4-alpha-glucan branching enzyme, C-terminal (BE_C)
Type: Domain

This entry represents the C-terminal domain found in bacterial 1,4-alpha-glucan branching enzymes (

), such as TTHA1902 from Thermus thermophilus and TK1436 from Thermococcus kodakarensis, which belong to the glycoside hydrolase family 57

. These enzymes catalyse the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. This is an α-helical domain composed of a four α-helical bundle and plays a role in the formation of the active-site cleft, being essential for substrate binding and catalysis .
Penicillin-binding protein 4, C-terminal domain (Pen-bd_prot4_C_dom)
Type: Domain

This domain is found towards the C terminus of prokaryotic penicillin-binding protein 4.
Carbohydrate binding module 27 (CBM27)
Type: Domain

This domain is found in carbohydrate binding proteins that bind to beta-1, 4-mannooligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. The region adopts a β sandwich structure comprising 13 β strands with a single, small α-helix and a single metal atom .
Chemokine-binding M3, viral (Chemokine-bd_M3_vir)
Type: Family

This entry represents a group of viral chemokine binding proteins, which 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.
Bacteriophage PRD1, P2, absorption protein (Phage_PRD1_P2)
Type: Family

This entry represents absorption protein P2 (synonym: receptor-binding protein P2) from the bacteriophage PRD1. Absorption protein P2 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 six-fold symmetry, and 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 .
Bacteriophage T4, Gp8 (Phage_T4_Gp8)
Type: Domain

Members of this family of viral baseplate structural proteins adopt a structure consisting of a three-layer β-sandwich with two finger-like loops containing an α-helix at the opposite sides of the sandwich. The two peripheral, five-stranded, antiparallel β-sheets are stacked against the middle, four-stranded, antiparallel β-sheet. Attachment of this family of proteins to the baseplate during assembly creates a binding site for subsequent attachment of Gp6 .
Gamete antigen, Plasmodium species (Gamete_antigen_PLAspp)
Type: Family

Members of this family are essential for gametocytogenesis in Plasmodium falciparum. They contain a fold composed of two pseudo dyad-related repeats of the helix-turn-helix motif, serving as a platform for RNA and Src homology-3 (SH3) binding .
DNA-binding pseudobarrel domain superfamily (DNA-bd_pseudobarrel_sf)
Type: Homologous_superfamily

This superfamily represents a DNA recognition domain found in the restriction endonuclease EcoRII and numerous transcription factors. The EcoRII structure has been studied and forms an eight-stranded β-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. The strands are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini β-sheets of four antiparallel β-strands, sheet I from β-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed β-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not .
Major coat protein, L-A virus (Major_coat_LA-virus)
Type: Domain

Members of this entry include the major coat protein of the Saccharomyces cerevisiae virus L-A (ScV-L-A) . The major coat protein is a large polypeptide without apparent domain division.
Fimbrial adhesin F17-AG, lectin domain (Fimbrial_adhesin_lectin_dom)
Type: Domain

This entry represents the carbohydrate-specific lectin domain found in bacterial fimbrial adhesins. It adopts a compact, elongated structure consisting of a β-sandwich with two major sheets: one consisting of five long strands in mixed orientations, and a front sheet with four antiparallel strands, forming an immunoglobin-like fold .
ZinT domain (ZinT_dom)
Type: Domain

This domain is found in prokaryotic proteins that were first identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium and ensure its subsequent elimination . Previously known YodA, these proteins have been renamed as ZinT, and have been shown to bind zinc with high affinity. They may play a role in zinc homeostasis and growth under zinc limited conditions .
Protein of unknown function DUF1961 (DUF1961)
Type: Family

Members of this family are found in a set of hypothetical bacterial proteins. Their exact function has not, as yet, been determined.
Restriction endonuclease, type II, PvuII (Restrct_endonuc_II_PvuII)
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 the type II restriction endonuclease PvuII, which recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3 .
Restriction endonuclease, type II, HincII (Restrct_endonuc_II_HincII)
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 the prokaryotic restriction endonuclease HincII, which recognises the double-stranded sequence 5'-GTYRAC-3' and cleave after Y-3 .
Bubble protein (Bubble)
Type: Family

This family includes Penicillium brevicompactum bubble protein (BP) and similar proteins. Bubble protein (BP) is a small cysteine-rich protein that is a member of the growing class of defensins, and may act as a toxin . Studies show that P. brevicompactum BP inhibits growth of the yeast Saccharomyces cerevisiae in a dose-dependent manner, thus exhibiting anti-fungal effects . BP may recognise a molecule or part of a molecule with a negatively charged surface. It is a globular protein consisting of several β-strands that are stabilised by disulfide bonds. .
Transcriptional repressor TraM (Tscrpt_rep_TraM)
Type: Family

Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel α-helices. These proteins can be divided into two parts, a globular head and an elongated tail, and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation .
Activator of Hsp90 ATPase AHSA1-like, N-terminal (AHSA1-like_N)
Type: Domain

This entry includes a group of heat shock protein interacting proteins, including AHSA1/2 from animals and Aha1/Hch1 from budding yeasts, and it represents a domain found at the N-terminal of Aha1 and AHSA1/2, while in Hch1 is the only domain. Aha1 adopts a secondary structure consisting of an N-terminal α-helix leading into a four-stranded meandering antiparallel β-sheet, followed by a C-terminal α-helix. The two α-helices are packed together, with the β-sheet curving around them. The N-terminal domain of Aha1 interacts with the central segment of Hsp90 which induces the conformational rearrangements of Hsp90 that favor the N-terminal domain-dimerized state of the chaperone and ends leads to the stimulation of its ATPase activity .

Activator of 90kDa heat shock protein ATPase Aha1/AHSA1 (AHSA1/p38,

) is known to interact with the middle domain of Hsp90, and stimulate its ATPase activity , where one Aha1/AHSA1 molecule per Hsp90 dimer is sufficient for this stimulation. It is probably a general up regulator of Hsp90 function, particularly contributing to its efficiency in conditions of increased stress . It is also known to interact with the cytoplasmic domain of the VSV G protein, and may thus be involved in protein transport . It has also been reported as being under expressed in Down's syndrome.

In budding yeasts, both Hch1 and Aha1 bind to the middle domain of Hsp90 and stimulate ATPase activity . However, Aha1 but not Hch1 stimulated the intrinsic ATPase activity of Hsp90 5-fold . Hch1 and Aha1 may regulate Hsp90 function in distinct ways .
DNA fragmentation factor 40, C-terminal (DFF40_C)
Type: Domain

Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans . In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death.

DNA fragmentation factor (DFF) is a complex of the DNase DFF40 (CAD) and its chaperone/inhibitor DFF45 (ICAD-L). In its inactive form, DFF is a heterodimer composed of a 45kDa chaperone inhibitor subunit (DFF45 or ICAD), and a 40kDa latent endonuclease subunit (DFF40 or CAD). Upon caspase-3 cleavage of DFF45, DFF40 forms active endonuclease homo-oligomers. It is activated during apoptosis to induce DNA fragmentation. DNA binding by DFF is mediated by the nuclease subunit, which can also form stable DNA complexes after release from DFF . The nuclease subunit is inhibited in DNA cleavage but not in DNA binding . DFF45 can also be cleaved and inactivated by caspase-7 but not by caspase-6 and caspase-8. The cleaved DFF45 fragments dissociate from DFF40, allowing DFF40 to oligomerise, forming a large complex that cleaves DNA by introducing double strand breaks. Histone H1 confers DNA binding ability to DFF and stimulates the nuclease activity of DFF40 .
Inner layer core protein VP3, Phytoreovirus (Innr_layr_core_VP3_Phytoreovir)
Type: Family

Members of this family are core structural proteins found in the double-stranded RNA virus Phytoreovirus. They are large proteins without apparent domain division, with a number of all-alpha regions and one all beta domain near the C-terminal end .
Protein Her-1 (Her-1)
Type: Family

Her-1 adopts an all-helical structure with two subdomains: residues 19-80 comprise a left-handed three-helix bundle with an overhand connection between the second and third helices, whilst residues 81-164 comprise a left-handed anti-parallel four-helix bundle in which the first helix consists of four consecutive turns of 3-10-helix. Fourteen Cys residues are conserved in all known HER-1 sequences and form seven disulphide bonds. The protein dictates male development in Caenorhabditis elegans, probably by playing a direct role in cell signalling during C. elegans sex determination. It also inhibits the function of tra-2a .
Restriction endonuclease, type II, EcoRV (Restrct_endonuc_II_EcoRV)
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 EcoRV prokaryotic restriction endonucleases, which recognise the double-stranded sequence 5'-GATATC-3' and cleave after T-3 .
Protein of unknown function DUF1963 (DUF1963)
Type: Family

This entry is a set of hypothetical proteins. Their function has not been described yet.
Ste50, sterile alpha motif (SAM_Ste50)
Type: Domain

Ste50-like proteins have a SAM domain at the N terminus and Ras-associated UBQ superfamily domain at the C terminus. They participate in regulation of mating pheromone response, invasive growth and high osmolarity growth response, and contribute to cell wall integrity in vegetative cells. Ste50 of S.cerevisiae acts as an adaptor protein between G protein and MAP triple kinase Ste11. Ste50 proteins are able to form homo-oligomers, binding each other via their SAM domains, as well as heterodimers and heterogeneous complexes with SAM domain or SAM homodimers of MAPKKK Ste11 protein kinase .

The fungal Ste50 SAM domain consists of five helices, which form a compact, globular fold. It is required for mediation of homodimerisation and heterodimerisation (and in some cases oligomerisation) of the protein .
Alpha-haemoglobin stabilising protein (A_Hb_stabilising_prot)
Type: Family

Alpha-haemoglobin stabilising protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three α-helix bundle .