SII-SWORD/CoKE huggingface dataset:
Pre-mRNA-processing factor 19, U-box domain (RING-Ubox_PRP19)
Type: Domain

This entry represents the U-box domain of Prp19.

Prp19, also known as DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signalling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex .

Prp19 is essential for spliceosome assembly and stability. It is a core component of the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome and participates in its assembly, its remodelling and is required for its activity. During assembly of the spliceosome, it mediates Lys-63-linked polyubiquitination of the U4 spliceosomal protein PRPF3. Ubiquitination of PRPF3 allows its recognition by the U5 component PRPF8 and stabilises the U4/U5/U6 tri-snRNP spliceosomal complex .

Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerisation and is essential for its auto-ubiquitination activity in vitro or when overexpressed , a coiled-coil Prp19 homology region that mediates its tetramerisation and interaction with CDC5L and SPF27 and a C-terminal seven-bladed WD40 β-propeller that forms an asymmetrical barrel-shaped structure important for substrate recognition and recruitment .
Herpesvirus glycoprotein B ectodomain C-terminal (Glycoprotein_B_ecto_C)
Type: Domain

This domain corresponds to the C-terminal region of the glycoprotein B ectodomain .

gB ectodomain has an elongated rod-like molecule, composed of five domains that contain both β-sheet and α-helical secondary structures. Domains 1 and 2 have a fold that resembles that of a plekstrin-homology (PH) domains. Domains 3, 4 and 5 (represented by this entry) have a more complex structure .

Glycoprotein B is an envelope glycoprotein that plays a role in host cell entry, cell to-cell virus transmission, and fusion of infected cells .
Rod shape-determining protein MreC, beta-barrel core (MreC_beta-barrel_core)
Type: Domain

This entry represents the periplasmic core of MreC and related proteins which is composed of two six-stranded β-barrels . MreC self-associates into polar filaments . The periplasmic part of MreC contains also a coiled-coil which is involved in the formation of dimer essential for its function .

MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped .
CREG-like, beta-barrel (CREG_beta-barrel)
Type: Domain

This entry represents the β-barrel domain found in CREG (cellular repressor of E1A-stimulated genes) proteins from animals and closely homologues from plants, fungi and bacteria . CREG is a secreted glycoprotein that inhibits proliferation and enhances differentiation of human embryonal carcinoma cells.

This domain has similarity to FMN-binding split barrel domains (

). It forms a tight homodimer that, unlike its closely related structural homologues, it does not bind flavin mononucleotide as the putative flavin mononucleotide-binding pocket in CREG is sterically blocked by a loop and several key bulky residues .

The structure of this domain from bacterial and plant proteins, revealed that it is involved in heme binding, such as

and

.
Protein-export membrane protein SecD/SecF, C-terminal, bacterial (SecD_SecF_C_bact)
Type: Domain

This entry represents the C-terminal domain of various prokaryotic SecD and SecF protein export membrane proteins. These SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC . SecD and SecF are required to maintain a proton motive force .
Large ribosomal subunit protein eL24-related, archaeal-type (Ribosomal_eL24-rel_arc)
Type: Family

This entry represents mammalian Large ribosomal subunit protein eL24 and related proteins from archaea.

Ribosomal protein eL24/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (eL24, distinct from archaeal L24). eL24/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. eL24/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination . L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis , and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development .

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 .
SUF system FeS cluster assembly, SufBD (Fe-S_cluster_assembly_SufBD)
Type: Family

Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.

The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.
U3 small nucleolar RNA-associated protein 6, N-terminal (UTP6_N)
Type: Domain

This entry represents the N-terminal segment of UTP6 proteins. This region contains repeats related to TPR superfamily repeats

.

Utp6 is a component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA .
Tripartite ATP-independent periplasmic transporters, DctQ component (DctQ)
Type: Domain

This entry includes tripartite ATP-independent periplasmic (TRAP) transporters which are substrate-binding protein (SBP)-dependent secondary transporters ubiquitous prokaryotes . They are comprised of an SBP of the DctP or TAXI families and two integral membrane proteins of unequal sizes that form the DctQ and DctM protein families (the small and large membrane components respectively) .

This entry represents the DctQ component and its homologues, which consists of five transmembrane segments. In SiaT, a protein involved in sialic acid uptake , this entry represents the N-terminal five transmembrane segments.
GIPC, GH2 (GH2_GIPC)
Type: Domain

The GIPC family includes PDZ domain-containing proteins, GIPC1 (also called GAIP C-terminus-interacting protein, RGS-GAIP-interacting protein, RGS19-interacting protein 1, RGS19IP1, synectin, tax interaction protein 2, or TIP-2), GIPC2, and GIPC3, which may act as scaffold proteins linking heterotrimeric G-proteins to seven-transmembrane-type WNT receptor or to receptor tyrosine kinases. They might play key roles in carcinogenesis and embryogenesis through modulation of growth factor signalling and cell adhesion . GIPCs proteins are composed of a GIPC homology 1 (GH1) domain, a central PDZ domain and a GH2 domain.

This entry corresponds to the GH2 domain, which mediates the interaction with myosin VI and is involved in homodimerization in the autoinhibited state .
Coiled-coil protein 142, C-terminal (CCDC142_C)
Type: Domain

This entry represents an α-helical ARM segment found at the C-terminal of CC142 proteins, whose function is unknown.
Urocanase (Urocanase)
Type: Family

Urocanase (also known as imidazolonepropionate hydrolase or urocanate hydratase) is the enzyme that catalyses the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate:

urocanate + H
2
O = 4,5-dihydro-4-oxo-5-imidazolepropanoate

Urocanase is found in some bacteria (gene hutU) , in the liver of many vertebrates, and has also been found in the plant Trifolium repens (white clover). Urocanase is a protein of about 60 Kd, it binds tightly to NAD
+
and uses it as an electrophil cofactor. A conserved cysteine has been found to be important for the catalytic mechanism and could be involved in the binding of the NAD
+
.

This enzyme is a symmetric homodimer with tightly bound NAD+ cofactors. Each subunit consists of a typical NAD-binding domain inserted into a larger core domain that forms the dimer interface .
aECM cysteine-cradle domain (CCD_aECM)
Type: Domain

This domain is found in nematode proteins that are known to be aECM (apical ExtraCellular Matrice) components. It is predicted to adopt a globular α-helical structure with a cradle-like shape. This domain contains four invariant cysteines which are probably involved in forming two disulfide bonds. The latter likely contribute to the maintenance of the cradle-like shape.
Domain of unknown function DUF7619 (DUF7619)
Type: Domain

This domain is found in uncharacterised proteins, sometimes in multiple copies. Some proteins containing this domain contain either LPXTG cell wall anchor motif

or secretion system C-terminal sorting domain

at the C terminus. It is likely that some members of this entry contain an intramolecular isopeptide bond.
Domain of unknown function DUF7507 (DUF7507)
Type: Domain

This domain of unknown function is found in multiple copies in a number of bacterial proteins. It is closely related to domains represented by DUF11 (

). Similarly to DUF11, this domain contains a conserved N-terminal lysine and a C-terminal asparagine with central aspartate/glutamate residues suggesting that it may contain an isopeptide bond. In addition, it contains a semi-conserved TNTGNV sequence motif in which a highly conserved asparagine probably plays a role in stabilising the rod structure formed by repetitive copies of this domain.
ZP-C domain (ZP-C)
Type: Domain

This entry represents the ZP-C domain which is the C-terminal structural domain that composes the Zona pellucida domain. This domain is predicted to adopt an Ig-like β-sandwich topology.

The zona pellucida (ZP) domain is a protein polymerisation module of ~260 amino acid module, which is found at the C terminus of many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer . Proteins containing a ZP domain include:

Sperm receptor proteins ZP2 and ZP3. Along with protein ZP1, proteins ZP2 and ZP3 are responsible for sperm-adhesion to the zona pellucida. ZP3 first binds to specific sperm proteins, thus mediating sperm contacts with the oocyte. ZP2 acts as a second sperm receptor reinforcing the interactions. ZP1 cross-links the polymers formed by ZP2 and ZP3.

Zona pellucida sperm-binding protein B (ZP-B) (also known as ZP-X in rabbit and ZP-3 α in pig).

Glycoprotein GP2, the major component of pancreatic secretory granule membranes.

TGF-beta receptor type III (also known as betaglycan). This protein is a proteoglycan that binds to TGF-beta and could be involved in capturing and retaining TGF-beta for presentation to the signalling receptors.

Uromodulin (also known as Tamm-Horsfall urinary glycoprotein). The function of this protein, which is the most abundant in human urine, is not yet clear.

Chicken beta-tectorin, a major glycoprotein of avian tectorial membrane.

Most ZP domain proteins are synthesized as precursors with carboxy-terminal transmembrane domains or glycosyl phosphatidylinositol (GPI) anchors .

The ZP domain contains eight strictly conserved cysteines, which form disulphide bridges. The disulphide bonds within the ZP domains are divided into two groups, suggesting that the ZP domain consists of two subdomains. In addition to the conserved cysteines, only a few aromatic or hydrophobic amino acids are absolutely invariant, probably as a result of structural rather than functional constraints .
ZP-N domain (ZP-N)
Type: Domain

This entry represents the ZP-N domain which is the N-terminal structural domain of the Zona pellucida domain. This domain is predicted to adopt an Ig-like β-sandwich topology.

The zona pellucida (ZP) domain is a protein polymerisation module of ~260 amino acid module, which is found at the C terminus of many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer . Proteins containing a ZP domain include:

Sperm receptor proteins ZP2 and ZP3. Along with protein ZP1, proteins ZP2 and ZP3 are responsible for sperm-adhesion to the zona pellucida. ZP3 first binds to specific sperm proteins, thus mediating sperm contacts with the oocyte. ZP2 acts as a second sperm receptor reinforcing the interactions. ZP1 cross-links the polymers formed by ZP2 and ZP3.

Zona pellucida sperm-binding protein B (ZP-B) (also known as ZP-X in rabbit and ZP-3 α in pig).

Glycoprotein GP2, the major component of pancreatic secretory granule membranes.

TGF-beta receptor type III (also known as betaglycan). This protein is a proteoglycan that binds to TGF-beta and could be involved in capturing and retaining TGF-beta for presentation to the signalling receptors.

Uromodulin (also known as Tamm-Horsfall urinary glycoprotein). The function of this protein, which is the most abundant in human urine, is not yet clear.

Chicken beta-tectorin, a major glycoprotein of avian tectorial membrane.

Most ZP domain proteins are synthesized as precursors with carboxy-terminal transmembrane domains or glycosyl phosphatidylinositol (GPI) anchors .

The ZP domain contains eight strictly conserved cysteines, which form disulphide bridges. The disulphide bonds within the ZP domains are divided into two groups, suggesting that the ZP domain consists of two subdomains. In addition to the conserved cysteines, only a few aromatic or hydrophobic amino acids are absolutely invariant, probably as a result of structural rather than functional constraints .
At1g61320/AtMIF1, LRR domain (LRR_At1g61320_AtMIF1)
Type: Domain

This entry represents the leucine-rich repeats (LRR) mainly found in plant proteins, such as At1g61320 and At1g61330 from Arabidopsis thaliana, which are F-box/LRR-repeat containing proteins involved in the ubiquitin-proteasome pathway. They function as components of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complexes . They have a F-box domain at the N-terminal (

). AtMIF1 (also known as F-box protein AT3G62230) from Arabidopsis, physically interacts with MYB domain protein 5 (MYB5), which results in MYB5 degradation representing a new regulatory pathway, 26S proteasome-AtMIF1-MYB5 that regulates oil content of seeds, increasing their oil content without affecting plant growth .
Clathrin heavy-chain repeat (CHCR)
Type: Repeat

This entry represents the CHCR found in the arm region of the Clathrin heavy chain.

Clathrin is a triskelion-shaped cytoplasmic protein that polymerises into a polyhedral lattice on intracellular membranes to form protein-coated membrane vesicles. Lattice formation induces the sorting of membrane proteins during endocytosis and organelle biogenesis by interacting with membrane-associated adaptor molecules. Clathrin functions as a trimer, and these trimers, or triskelions, are comprised of three legs joined by a central vertex. Each leg consists of one heavy chain and one light chain. The clathrin heavy-chain contains a 145-residue repeat that is present in seven copies . The clathrin heavy-chain repeat (CHCR) is also found in nonclathrin proteins such as Pep3, Pep5, Vam6, Vps41, Vps8 from Saccharomyces cerevisiae and their orthologues from other eukaryotes such as Vps11 in zebra fish . These proteins, like clathrins, are involved in vacuolar maintenance and protein sorting. The CHCR repeats in these proteins could mediate protein-protein interactions, or possibly represent clathrin-binding domains, or perform clathrin-like functions. CHCR repeats in the clathrin heavy chain, Saccharomyces cerevisiae Vamp2 and human Vamp6 have been implicated in homooligomerization, suggesting that this may be the primary function of this repeat.

The CHCR repeat folds into an elongated right-handed superhelix coil of short α-helices . Individual 'helix-turn-helix-loop' or helix hairpin units comprise the canonical repeat and stack along the superhelix axis to form a single extended domain. The canonical hairpin repeat of the clathrin superhelix resembles a tetratrico peptide repeat (TPR), but is shorter and lacks the characteristic spacing of the hydrophobic residues in TPRs.
60S ribosome subunit biogenesis protein Nip7, pre-PUA domain, eukaryotes (Nip7_N_euk)
Type: Domain

Human 60S ribosome subunit biogenesis protein NIP7 homologue (also known as KD93) is essential in the accurate processing of pre-rRNA . The overall fold of KD93 consists of two interlinked α/β domains. The C-terminal domain resembles the PUA domain of some RNA modification enzymes, especially that of archaeosine tRNA-ribosyltransferase (ArcTGT), suggesting a possible molecular function related to RNA binding .

This entry represents the N-terminal, pre-PUA domain of NIP7 from eukaryotes.
bAvd-like (bAvd)
Type: Domain

This entry includes accessory variability determinant bAvd protein from Bordetella phage BPP-1 and similar sequences from tailed bacteriophages and proteobacterial prophages. bAvd proteins are encoded by diversity-generating retroelements (DGR). They transfer coding information from a template region through an RNA intermediate to a protein-encoding variable region and generates protein sequence variation to provide the phage with the capacity to adapt to its host. The reverse transcription by the DGR is carried out by a complex of reverse transcriptase bRT and bAvd proteins. bAvd forms a positively charged pentameric, barrel-shaped structure, with one end narrower than the other .
tRNA (guanine-N(7)-)-methyltransferase TrmB, bacteria (tRNA_methyltr_TrmB_bact)
Type: Family

This entry represents tRNA (guanine-N-7) methyltransferase (

) mainly from bacteria, which catalyses the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. Capping of the pre-mRNA 5' end by addition a monomethylated guanosine cap (m(7)G) is an essential and the earliest modification in the biogenesis of mRNA . The reaction is catalysed by three enzymes: triphosphatase, guanylyltransferase, and tRNA (guanine-N-7) methyltransferase . This entry includes Bacillus subtilis TrmB, which contains a unique variant of the Rossmann-fold methyltransferase (RFM) structure, with the N-terminal helix folded on the opposite site of the catalytic domain . This entry also includes the bifunctional methyltransferase RFTRM from Rickettsia, in which this activity is found at the C-terminal.
PTHB1, platform domain (PTHB1_pf_dom)
Type: Domain

This entry represents the platform domain found in PTHB1 protein and PTHB1 homolog from C. elegans.

PTHB1 (also known as Bardet-Biedl syndrome 9 protein, BBS9) forms a part of the BBSome complex, which is required for ciliogenesis . PTHB1 is the major binding subunit of the IFT38 C-terminal tail, which assists the BBSome in some of its roles .
PTHB1, hairpin domain (PTHB1_hp_dom)
Type: Domain

This entry represents a hairpin domain found in PTHB1 protein and PTHB1 homolog from C. elegans.

PTHB1 (also known as Bardet-Biedl syndrome 9 protein, BBS9) forms a part of the BBSome complex, which is required for ciliogenesis . PTHB1 is the major binding subunit of the IFT38 C-terminal tail, which assists the BBSome in some of its roles .
PTHB1, C-terminal helix bundle domain (PTHB1_CtH_dom)
Type: Domain

This entry represents the C-terminal helix bundle (CtH) found in PTHB1 protein.

PTHB1 (also known as Bardet-Biedl syndrome 9 protein, BBS9) forms a part of the BBSome complex, which is required for ciliogenesis . PTHB1 is the major binding subunit of the IFT38 C-terminal tail, which assists the BBSome in some of its roles .
Sublancin immunity protein SunI-like, PH domain (PH_SunI-like)
Type: Domain

Bacillus subtilis strain 168 produces the lantibiotic sublancin 168, a broad spectrum bacteriocin. SunI has been identified as the sublancin immunity protein. It belongs to a novel class of bacteriocin antagonists with a particular topology consisting of one N-terminal transmembrane domain and the bulk of the protein facing the cytoplasm . This entry also includes Bacillus subtilis protein YnzG and related UPF0457 proteins from Staphylococcus sp, whose function is unknown.