SII-SWORD/CoKE huggingface dataset:
Ascorbate oxidase, second cupredoxin domain (CuRO_2_AAO)
Type: Domain

Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. This multicopper oxidase (MCO) is found in cucurbitaceous plants such as pumpkin, cucumber, and melon. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear ; some studies suggest that it may play a crucial role in cell elongation and enlargement . In pumpkin, its expression is increased during callus growth, fruit development and seedling elongation .

MCOs couple oxidation of substrates with reduction of dioxygen to water. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper centre. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre . The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper.
Ascorbate oxidase, first cupredoxin domain (CuRO_1_AAO)
Type: Domain

Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. This multicopper oxidase (MCO) is found in cucurbitaceous plants such as pumpkin, cucumber, and melon. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear ; some studies suggest that it may play a crucial role in cell elongation and enlargement . In pumpkin, its expression is increased during callus growth, fruit development and seedling elongation .

MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3 .
Yme2, RNA recognition motif (Yme2_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of Yme2 (Mitochondrial escape protein 2), which is an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions . In Saccharomyces cerevisiae, it may serve as a mediator of nucleoid structure and number in mitochondria . Yme2 contains an exonuclease domain and an RNA recognition motif (RRM).
CNOT4, RNA recognition motif (CNOT4_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of NOT4 (also known as CNOT4), which is a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription . NOT4 functions as an ubiquitin-protein ligase (E3) . It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions .
TRMT2A, RNA recognition motif (TRMT2A_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of TRMT2A (tRNA (uracil-5-)-methyltransferase homologue A), which is a cell cycle regulated protein that has been associated with the clinical outcome in HER2 expressing breast cancer . The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM).
Ephrin type-A receptor 2, ligand binding domain (EphA2_rcpt_lig-bd)
Type: Domain

This entry represents the ligand-binding domain found in ephrin type-A receptor 2 (EphA2). EphA2 negatively regulates cell differentiation and has been shown to be overexpressed in tumor cells and tumor blood vessels in a variety of cancers including breast, prostate, lung, and colon. As a result, it is an attractive target for drug design since its inhibition could affect several aspects of tumor progression .

Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands .

Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling) .
RBM48, RNA recognition motif (RBM48_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of RBM48, a putative RNA-binding protein of unknown function. It contains one RNA recognition motif (RRM) .
MCM3AP, RNA recognition motif (MCM3AP_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of MCM3-associated protein (MCM3AP, also known as GANP), a nuclear protein with multiple domains, which have different functions. GANP serves as the scaffold of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export . GANP can act as an RNA export factor that interacts with activation-induced cytidine deaminase (AID) and shepherds it from the cytoplasm to the nucleus, and toward the IgV region loci in B cells .

GANP contains the Sac3-homology domain, a putative RNA recognition motif, the Nup-homology domain, and the C-terminal histone-acetyltransferase (HAT) domain. Its HAT domain has been shown to regulate minichromosome maintenance protein 3 (MCM3) . An alternatively spliced variant of GANP mRNA has been reported in humans. A shorter isoform of GANP (likely to encode an 80kDa protein) is associated with MCM3 of the DNA helicase MCM-complex (composed of MCM2-MCM7) and possesses HAT activity .
Ephrin type-A receptor 3, ligand binding domain (EphA3_rcpt_lig-bd)
Type: Domain

This entry represents the ligand-binding domain found in ephrin type-A receptor 3 (EphA3). EphA3 has also been implicated in lung tumors .

Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands .

Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling) .
Ascorbate oxidase, third cupredoxin domain (CuRO_3_AAO)
Type: Domain

Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. This multicopper oxidase (MCO) is found in cucurbitaceous plants such as pumpkin, cucumber, and melon. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear ; some studies suggest that it may play a crucial role in cell elongation and enlargement . In pumpkin, its expression is increased during callus growth, fruit development and seedling elongation .

MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3 .
RBM25, RNA recognition motif (RBM25_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) of RBM25, which is a RNA-binding protein that acts as a regulator of alternative pre-mRNA splicing. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor . It has been shown to function in cardiac sodium channel splicing regulation of human heart failure .

RBM25 contains a well conserved RNA recognition motif (RRM), at the N terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif.
At5g42320-like, carboxypeptidase domain (At5g42320_M14_CPD)
Type: Domain

This entry represents the carboxypeptidase domain found in a functionally uncharacterised subgroup of the M14 family of metallocarboxypeptidases (MCPs), including the At5g42320 gene product of
Arabidopsis thaliana
.
Ephrin type-A receptor 4, ligand binding domain (EphA4_rcpt_lig-bd)
Type: Domain

This entry represents the ligand-binding domain found in ephrin type-A receptor 4 (EphA4). A loss of EphA4, as well as EphB2, precedes memory decline in a murine model of Alzheimers disease . EphA4 has been shown to have a negative effect on axon regeneration and functional restoration in corticospinal lesions and has been implicated in circadian sleep regulation .

Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands .

Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling) .
Ascorbate oxidase homologue, second cupredoxin domain (CuRO_2_AO-like)
Type: Domain

The proteins in this subfamily share homology to ascorbate oxidase and other members of the blue copper oxidase family. Expression of protein NTP303 from Nicotiana tabacum is detected during germination and pollen tube growth . Ascorbate oxidase is a member of the multicopper oxidase (MCO) family that couples oxidation of substrates with reduction of dioxygen to water.

Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper centre. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper .
Ascorbate oxidase homologue, first cupredoxin domain (CuRO_1_AAO-like)
Type: Domain

The proteins in this subfamily share homology to ascorbate oxidase and other members of the blue copper oxidase family. Expression of protein NTP303 from Nicotiana tabacum is detected during germination and pollen tube growth . Ascorbate oxidase is a member of the multicopper oxidase (MCO) family that couples oxidation of substrates with reduction of dioxygen to water.

MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. This subfamily does not harbour trinuclear copper binding histidines .
ENP1, carboxypeptidase domain (ENP1_M14_CPD)
Type: Domain

This entry represents the carboxypeptidase domain found in gamma-D-glutamyl-L-diamino acid endopeptidase 1 (also known as ENP1, (

); MEROPS identifier M14.008). ENP1 is a member of subfmaily M14C of the M14 family of metallocarboxypeptidases (MCPs) . However, it has an exceptional type of activity of hydrolyzing the gamma-D-Glu-(L)meso-diaminopimelic acid (gamma-D-Glu-Dap) bond of L-Ala-gamma-D-Glu-(L)meso-diaminopimelic acid and L-Ala-gamma-D-Glu-(L)meso-diaminopimelic acid(L)-D-Ala peptides. ENP1 has a different substrate specificity and cellular role than MpaA (MpaA does not belong to this group). ENP1 hydrolyzes the gamma-D-Glu-Dap bond of MurNAc-tripeptide and MurNAc-tetrapeptide, as well as the amide bond of free tripeptide and tetrapeptide. ENP1 is active on spore cortex peptidoglycan, and is produced at stage IV of sporulation in forespore and spore integuments .
Ascorbate oxidase homologue, third cupredoxin domain (CuRO_3_AO-like)
Type: Domain

The proteins in this subfamily share homology to ascorbate oxidase and other members of the blue copper oxidase family. Expression of protein NTP303 from Nicotiana tabacum is detected during germination and pollen tube growth . Ascorbate oxidase is a member of the multicopper oxidase (MCO) family that couples oxidation of substrates with reduction of dioxygen to water.

MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part of the trinuclear copper binding site, which is located at the interface of domains 1 and 3. This subfamily does not harbour T1 copper or trinuclear copper binding sites .
Gar2, RNA recognition motif 2 (Gar2_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of yeast protein Gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation . It shares similar domain architecture with nucleolin from vertebrates and Nsr1 from Saccharomyces cerevisiae . The highly phosphorylated N-terminal domain of Gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of Gar2 contains two closely adjacent RNA recognition motifs (RRMs). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues .
Ephrin type-A receptor 5, ligand binding domain (EphA5_rcpt_lig-bd)
Type: Domain

This entry represents the ligand-binding domain found in ephrin type-A receptor 5 (EphA5), also known as brain-specific kinase (Bsk). EphA5 is almost exclusively expressed in the nervous system, and is thought to play a role in synaptogenesis, and in dorsoventral organization of the spinal cord .

Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands .

Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling) .
RBM3/CIRBP, RNA recognition motif (RBM3/CIRBP_RRM)
Type: Domain

This entry represents the RNA recognition motif (RRM) domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also known as CIRP) and RBM3, both of which belong to a highly conserved cold shock proteins family, characterised by an N-terminal RNA-binding domain and a C-terminal arginine-glycine-rich (RGG) domain . CIRBP and RBM3 are key factors during early development. They can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. Despite the similarities between both CIRBP and RBM3 proteins, their biological functions are distinct .
Copper resistance protein, third cupredoxin domain (CuRO_3_CopA)
Type: Domain

CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes . CopA mutant causes a loss of function including copper tolerance and oxidase activity and copA transcription is inducible in the presence of copper .

Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper centre. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3 .
Ephrin type-A receptor 6, ligand binding domain (EphA6_rcpt_lig-bd)
Type: Domain

This entry represents the ligand-binding domain found in ephrin type-A receptor 6 (EphA6). EphA6, like other Eph receptors and their ephrin ligands, seems to play a role in neural development, underlying learning and memory . EphA6 has also been implicated in retinal vascular patterning .

Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands .

Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling) .
Copper resistance protein CopA, second cupredoxin domain (CuRO_2_CopA)
Type: Domain

CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes . CopA mutant causes a loss of function including copper tolerance and oxidase activity and copA transcription is inducible in the presence of copper .

Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper centre. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper .
Ephrin type-A receptor 7, ligand binding domain (EphA7_rcpt_lig-bd)
Type: Domain

This entry represents the ligand-binding domain found in ephrin type-A receptor 7 (EphA7). EphA7 has been implicated in various cancers, including lung, prostate, as well as leukemia . EphA7 has also been suggested to play a role in the development and maintenance of cortical domains within the cerebral cortex .

Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands .

Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling) .
Copper resistance protein, first cupredoxin domain (CuRO_1_CopA)
Type: Domain

CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes . CopA mutant causes a loss of function including copper tolerance and oxidase activity and copA transcription is inducible in the presence of copper .

Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper centre. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3 .
Laccase, second cupredoxin domain (CuRO_2_LCC)
Type: Domain

Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Plants usually express multiple laccase genes, but their precise physiological/biochemical roles remain largely unclear . In cotton (Gossypium spp.), laccases may be involved in fibre development .

Like other related multicopper oxidases (MCOs), laccase is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper centre. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to the active site trinuclear copper centre. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper .
Cytosolic carboxypeptidase-like protein 5 catalytic domain (M14_AGBL5-like)
Type: Domain

This entry contains the M14 carboxypeptidase-like domain of cytosolic carboxypeptidase-like protein 5 (CCP5, ATP/GTP binding protein-like 5 or AGBL-5; MEROPS identifier M14.025), and related proteins. CCP5 is part of the cytosolic carboxypeptidase (CCP) family, which also includes enzymes CCP1/Nna1, CCP4, and CCP6 , and belongs to subfamily M14B of peptidase family M14 . CCP5 removes alpha- and gamma-linked glutamates from tubulin .