SII-SWORD/CoKE huggingface dataset:
PELP1, middle domain (PELP1_middle)
Type: Domain

This entry represents a middle domain found in PELP1 (Proline-, glutamic acid- and leucine-rich protein 1, also known as modulator of nongenomic activity of estrogen receptor) which consists of HEAT repeats . PELP1 is a coactivator of estrogen receptor-mediated transcription and a corepressor of other nuclear hormone receptors and sequence-specific transcription factors . It forms the Five Friends of Methylated Chtop (5FMC) nuclear complex, together with the Sumo-specific protease Senp3, Wdr18, Tex10, and Las1L, in which it constitutes the core of 5FMC . This complex is recruited by Chromatin target of Prmt1 (Chtop, a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation) when the latter is arginine-methylated by Prmt1.
PIH1, N-terminal (PIH1_N)
Type: Domain

Proteins containing this domain include kintoun, Saccharomyces cerevisiae PIH1 (protein interacting with Hsp90 1, also known as Nop17) and PIH1 domain-containing proteins.
PARP1-like, PADR1 domain, zinc ribbon fold (PARP1-like_PADR1_Zn_ribbon)
Type: Domain

This entry represents the zinc-ribbon fold of PADR1 domain .

Poly(ADP-ribose) polymerase-1 (PARP-1) is a chromatin-associated enzyme involved in multiple cellular processes including DNA repair, cell cycle control, apoptotic signalling, and transcriptional regulation. Stimulated by binding to nicked DNA, PARP-1 catalyses poly(ADP-ribosyl)ation of the acceptor proteins using NAD as a substrate. PARP-1 has a modular architecture composed of multiple, independently folded domains that can be generally described in three major segments representing the biochemical activities and functional roles of the enzyme: the DNA-binding domain (DBD), the automodification domain which contains a BRCT fold, and the catalytic domain, which consists of the helical (HD) and the ART subdomains. The catalytic domain of PARP-1 is located at the C-terminal end of the protein. The DNA-binding domain is located at the N terminus of PARP-1 and contains two zinc fingers that bind to various DNA structures, a nuclear localization signal, and a caspase-3 cleavage site. The two N-terminal zinc fingers of PARP-1 bind to DNA structures to trigger activation of the C-terminal catalytic domain of PARP-1. The DBD of human PARP-1 contains yet a third zinc-binding domain, referred to as PADR1, located between the N-terminal PARP-type zinc fingers and the central BRCT domain and it is required to mediate interdomain contacts essential for the efficient assembly of PARP-1 domains .

The fold of the PADR1 zinc-binding domain consists of an N-terminal helical region, a central zinc ribbon fold, and a C-terminal tail. Three α-helices form a subdomain at the N terminus, with the first helix extending away from the subdomain. The zinc-binding region forms a separate subdomain, making primarily water-mediated contacts with the N-terminal helical subdomain. The zinc-binding subdomain resembles a zinc ribbon fold with four Cys ligands. The spacing between the four Cys residues is strongly conserved among all organisms, following the pattern C-x(2)-C-x(11,12)-C-x(9)-C where C is cysteine and x(n) is the number of amino acids between the Cys
residues. The zinc-binding subdomain contains a three-stranded antiparallel β-sheet, with the first pair of zinc ligands located in the loop running over the top of the sheet. The other pair of zinc ligands is centrally located within β-strands, a result of a long (nine-amino acid) insertion between the third and fourth cysteines. An α-helix on the C-terminal tail of the PADR1 zinc-binding domain contributes to the fold of the N-terminal helical region, and the remainder of the C terminus extends away from the N-terminal subdomain .
PHR (PHR)
Type: Domain

This domain is called PHR as it was originally found in the E3 ubiquitin-protein ligase proteins PAM (

), highwire (

) and RPM-1 (

) .

PHR proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterised by the presence of two PHR domains near the N terminus, which are essential for proper localisation and function. The domain has a β-sandwich fold composed of 11 anti-parallel β-strands .

The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils .
PROCT domain (PROCT)
Type: Domain

The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family .
Peptidase S64, Ssy5 (Peptidase_S64_Ssy5)
Type: Family

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .

This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1 and belongs to MEROPS petidase family S64 (clan PA). The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS peptidase family S1) and to have a typical trypsin-like catalytic triad .
Photosystem I PsaX (PSI_PsaX)
Type: Family

This family consists of the PsaX family of photosystem I (PSI) protein subunits. PSI is a large multi-subunit pigment protein complex embedded in the thylakoid membranes of green plants and cyanobacteria. PsaX is one of the 12 protein subunits found in PSI and these subunits are arranged as monomers or trimers within the membrane as shown by the structure of the trimeric complex from Synechococcus elongatus .
ROK, N-terminal (ROK_N)
Type: Domain

This presumed domain is found at the N terminus of RNP K-like proteins that also contain KH domains

.
Large ribosomal subunit protein uL30, N-terminal, eukaryotes (Ribosomal_uL30_N_euk)
Type: Domain

This presumed domain is found at the N terminus of the large ribosomal subunit protein uL30 from eukaryotes and has been termed RL30NT or NUC018 .

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 .
SEP domain (SEP_domain)
Type: Domain

The SEP (after shp1, eyc and p47) domain is an eukaryotic domain, which occurs frequently and mainly in single units. Almost all proteins containing a SEP domain are succeeded closely by a UBX domain (see

). The function of the SEP domain is as yet unknown but it has been proposed to act as a reversible competitive inhibitor of the lysosomal cysteine protease cathepsin L .

The sructure of the SEP domain comprises a β-sheet composed of four strands, and two α-helices. One side of the β-sheet faces alpha1 and alpha2. The longer helix alpha1 packs against the four-stranded β-sheet, where as the shorter helix alpha2 is located at one edge of the globular structure formed by alpha1 and the four stranded β sheet. A number of highly conserved hydrophobic residues are present in the SEP domain, which are predominantly buried and form the hydrophobic core .

Some proteins known to contain a SEP domain are listed below:

Eukaryotic NSFL1 cofactor p37 (or p97 cofactor p37), an adapter protein required for Golgi and endoplasmic reticulum biogenesis. It is involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis.

Eukaryotic NSFL1 cofactor p47 (or p97 cofactor p47), a major adaptor molecule of the cytosolic AAA-type ATPase (ATPases associated with various cellular activities) p97. p47 is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus.

Vertebrate UBX domain-containing protein 4 (UBXD4).

Plant UBA and UBX domain-containing protein.

Saccharomyces cerevisiae (Baker's yeast) UBX domain-containing protein 1 or Suppressor of high-copy PP1 protein (shp1), the homologue of p47.

Drosophila melanogaster (Fruit fly) eyes closed (eyc).
Sec23/Sec24, beta-sandwich (Beta-sandwich_Sec23_24)
Type: Domain

COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex . COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation .

Sec23 p and Sec24p are structurally related, folding into five distinct domains: a β-barrel, a zinc-finger (

), an α/β trunk domain (

), an all-helical region (

), and a C-terminal gelsolin-like domain (

). This entry describes part of the Sec23/24 β-barrel domain, which is formed from approximately 180 residues from three segments of the polypeptide. The strands of the barrel are oriented roughly parallel to the membrane such that one end of the barrel forms part of the inner surface of the coat and the other end part of the membrane-distal surface. The barrel is constructed from two opposed sheets: a six-stranded β-sheet facing partly towards the zinc finger domain and partly towards the solvent, and a five-stranded β-sheet facing the helical domain.
UME domain (UME)
Type: Domain

This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1 .
Membrane bound YbgT-like (YbgT_YccB)
Type: Family

This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in Escherichia coli. Members have a consensus motif (MWYFXW), which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to proteobacteria .
CIII regulator (CIII_regul)
Type: Family

This family consists of the CIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda CIII stabilises the lambda CII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon .
Zinc finger, CHHC-type (Znf_CHHC)
Type: Domain

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents a putative zinc-binding domain (CHHC motif) in RNP H and F. The domain is often associated with

.
Rare lipoprotein A (RplA)
Type: Domain

Rare lipoprotein A (RlpA) is an outer membrane protein that localises to the septal ring and scattered foci along the lateral wall in Escherichia coli. In Pseudomonas aeruginosa, RlpA is a lytic transglycosylase with preference for naked glycan strands that is needed for efficient separation of daughter cells and maintenance of rod shape .

This entry represents a conserved region in RlpA and RlpA-like proteins.
Pyridine nucleotide-disulphide oxidoreductase, class I, active site (Pyr_OxRdtase_I_AS)
Type: Active_site

The pyridine nucleotide-disulphide oxidoreductases are FAD flavoproteins which contain a pair of redox-active cysteines involved in the transfer of reducing equivalents from the FAD cofactor to the substrate. On the basis of sequence and structural similarities these enzymes can be classified into two categories. The first category groups together the following enzymes :

Glutathione reductase (

) (GR).

Higher eukaryotes thioredoxin reductase (

).

Trypanothione reductase (

).

Lipoamide dehydrogenase (

), the E3 component of alpha-ketoacid dehydrogenase complexes.

Mercuric reductase (

).

The sequence around the two cysteines involved in the redox-active disulphide bond is conserved and can be used as a signature pattern.

Note: In positions 6 and 7 of the pattern all known sequences have Asn-(Val/ Ile) with the exception of GR from plant chloroplasts and from cyanobacteria which have Ile-Arg .
Large ribosomal subunit protein uL4, eukaryotic/archaeal, conserved site (Ribosomal_uL4_euk/arc_CS)
Type: Conserved_site

This entry represents a conserved region found at the N-terminal of eukaryotic and archaeal large ribosomal subunit protein uL4 (also known as L4/L1. L4 from yeast has been shown to bind rRNA .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Large ribosomal subunit protein uL4-like (Ribosomal_uL4-like)
Type: Family

This family includes bacterial Large ribosomal subunit protein uL4 and eukaryotic Large ribosomal subunit protein uL4c/m (also known as L4) .

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 .
Antimicrobial peptide, C6 type, conserved site (Antimicrobial_C6_CS)
Type: Conserved_site

Plants normally grow on substrates that are extremely rich in microorganisms, but infection remains a rare event. During evolution, plants have developed a variety of defence systems to protect themselves from potential pathogens. Proteins including thionins, plant defensins and chitinases have been shown to play active roles against pathogen infections. Plants produce a wide array of antimicrobial compounds for escaping from microorganisms, which have antibacterial, anti-fungal activity, etc. Antimicrobial peptides extracted from plants inhibit the growth of a variety of fungi, oomycetes, Gram-positive bacterial phytopathogenes and Saccharomyces cerevisiae (Baker's yeast). Many antimicrobial peptides (AMPs) which contain cysteine residues abundantly have been isolated from plants, and these are classified into the plant defensin family. Plant defensins can be classified broadly into three types (hevein type, C6 type, and C8 type) according to the number and the position of cysteine residues in the molecules. The C6 type of plant defensins are highly basic proteins that contain 6 cysteine residues and a continuous sequence of cysteines (-CC-). All the 6 cysteines are involved in disulphide bond formation for stabilising protein tertiary structure .