SII-SWORD/CoKE huggingface dataset:
C-mannosyltransferase Dpy19 (Dpy19)
Type: Family

This entry represents a group of proteins from invertebrates, including C-mannosyltransferase dpy-19 from Caenorhabditis elegans. Dpy19 are transmembrane domain proteins whose name is derived from the Caenorhabditis elegans Dumpy mutant. They are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen .
C-mannosyltransferase Dpy-19-like protein 1 (Dpy19L1)
Type: Family

This entry represents a C-mannosyltransferase known as Dpy-19-like protein 1 (DPY19L1).

Dpy19 proteins are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen. Dpy19 is a transmembrane domain family whose name is derived from the Caenorhabditis elegans Dumpy mutant .
C-mannosyltransferase Dpy-19-like protein 4 (Dpy19L4)
Type: Family

This entry represents a probable C-mannosyltransferase by its similarity to Dpy-19. It is known as Dpy-19-like protein 4 (DPY19L4).

Dpy19 proteins are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen. Dpy19 is a transmembrane domain family whose name is derived from the Caenorhabditis elegans Dumpy mutant .

The function of Dpy19L4 (also called protein Dpy-19 homologue 4) is unknown .
C-mannosyltransferase Dpy-19-like protein 3 (Dpy19L3)
Type: Family

This entry represents a probable C-mannosyltransferase by its similarity to Dpy-19. It is known as Dpy-19-like protein 3 (DPY19L3).

Dpy19 proteins are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen. Dpy19 is a transmembrane domain family whose name is derived from the Caenorhabditis elegans Dumpy mutant .
E3 ubiquitin-protein ligase UHRF2, RING finger, HC subclass (RING-HC_UHRF2)
Type: Domain

This entry represents the C3HC4-type RING-HC finger of UHRF2 and similar sequences from vertebrates.

E3 ubiquitin-protein ligase UHRF2, also called Np95/ICBP90-like RING finger protein (NIRF) or Np95-like RING finger protein, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination . It also ubiquitinates PCNP, a PEST-containing nuclear protein . UHRF2 also functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis . It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation . Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation .

UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger domain.
E3 ubiquitin-protein ligase UHRF2, PHD finger (PHD_UHRF2)
Type: Domain

This entry represents the PHD finger of UHRF2 and similar sequences from vertebrates.

E3 ubiquitin-protein ligase UHRF2, also called Np95/ICBP90-like RING finger protein (NIRF) or Np95-like RING finger protein, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination . It also ubiquitinates PCNP, a PEST-containing nuclear protein . UHRF2 also functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis . It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation . Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation .

UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger domain.
E3 ubiquitin-protein ligase UHRF2, ubiquitin-like domain (Ubl_UHRF2)
Type: Domain

This entry represents the ubiquitin-like (Ubl) domain of UHRF2 and similar sequences from vertebrates.

E3 ubiquitin-protein ligase UHRF2, also called Np95/ICBP90-like RING finger protein (NIRF) or Np95-like RING finger protein, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination . It also ubiquitinates PCNP, a PEST-containing nuclear protein . UHRF2 also functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis . It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation . Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation .

UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger domain.
Diacylglycerol kinase alpha, second protein kinase C conserved region 1 (C1_DGKalpha_rpt2)
Type: Domain

This entry represents the second protein kinase C conserved region 1 (C1 domain) of DAG kinase alpha and similar proteins from vertebrates. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn2-binding sites.

Diacylglycerol (DAG) kinase (

) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase alpha, also called 80 kDa diacylglycerol kinase, or diglyceride kinase alpha (DGK-alpha), converts the second messenger diacylglycerol into phosphatidate upon cell stimulation, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. This protein plays a role in cell cycle progression . DAG kinase alpha acts as a negative modulator of diacylglycerol-based signals during T cell activation . It is involved in cancer development as it has been found upregulated in several types of cancer which leads to hyporesponsiveness or anergy of T cells, a mechanism used by tumours to avoid the immune system . This protein is also important for the generation of phosphatidic acid required for tubular recycling endosome (TRE) biogenesis .

It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca2 and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DAG kinase alpha contains two copies of the C1 domain which are essential for plasma membrane targeting of the protein in intact cells .
Diacylglycerol kinase beta, second protein kinase C conserved region 1 (C1_DGKbeta_rpt2)
Type: Domain

This entry represents the second protein kinase C conserved region 1 (C1 domain) of DAG kinase beta and similar proteins from vertebrates. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn2-binding sites.

Diacylglycerol (DAG) kinase (

) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase beta, also called 90 kDa diacylglycerol kinase, or diglyceride kinase beta (DGK-beta), exhibits high phosphorylation activity for long-chain diacylglycerols. It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca2 and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DAG kinase beta contains two copies of the C1 domain, which bind DAG and phorbol esters . This enzyme is specifically expressed in brain and regulates neuron-specific morphological changes including neurite branching and neurite spine formation .
Diacylglycerol kinase beta-like, first protein kinase C conserved region 1 (C1_DGKbeta-like_rpt1)
Type: Domain

This entry represents the first protein kinase C conserved region 1 (C1 domain) of DAG kinase beta and similar proteins from vertebrates and arthropods. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn2-binding sites.

Diacylglycerol (DAG) kinase (

) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase beta, also called 90 kDa diacylglycerol kinase, or diglyceride kinase beta (DGK-beta), exhibits high phosphorylation activity for long-chain diacylglycerols. It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca2 and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DAG kinase beta contains two copies of the C1 domain, which bind DAG and phorbol esters . This enzyme is specifically expressed in brain and regulates neuron-specific morphological changes including neurite branching and neurite spine formation .

Diacylglycerol kinase 1 (DGK1), the DAG kinase beta orthologue from Drosophila melanogaster, is also included in this entry. Upon cell stimulation DGK1 converts the second messenger diacylglycerol into phosphatidate, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. It may have a role in the development of the embryonic nervous system and the function of the adult nervous system and muscle, regulating signal transduction in neurons .
ARID4A, first Tudor domain (Tudor_ARID4A_rpt1)
Type: Domain

The N-terminal region of ARID4A has interdigitated double Tudor domains similar to the Jmjc domain-containing histone demethylase (JMJD2A), which has double-stranded DNA-binding activity and is well conserved throughout animals . This entry represents the first Tudor domain of ARID4A and similar sequences from vertebrates.

ARID4A, also called retinoblastoma-binding protein 1 (RBBP1 or RBP1), is a leukaemia and tumour suppressor involved in epigenetic regulation in leukaemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodelling complex through its interaction with the breast cancer associated tumour suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homologue ARID4B (also known as RBP1L1) . ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities . It also acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade .

ARID4A contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain . The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only the chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodelling and epigenetic regulation.
ARID4A, chromo barrel domain (CBD_RBP1-like)
Type: Domain

This entry represents the chromo barrel domain of ARID4A, which is a member of the chromo-like superfamily that includes chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. This is a typical SH3-fold-β-barrel domain with sequence similarity to the canonical chromodomain . The chromo barrel domain of ARID4A has DNA binding and methylated histone tail binding activities .

ARID4A, also called retinoblastoma-binding protein 1 (RBBP1 or RBP1), is a leukaemia and tumour suppressor involved in epigenetic regulation in leukaemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodelling complex through its interaction with the breast cancer associated tumour suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homologue ARID4B (also known as RBP1L1) . ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities . It also acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade .

ARID4A contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain . The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only the chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodelling and epigenetic regulation.
ARID4B, second Tudor domain (Tudor_ARID4B_rpt2)
Type: Domain

This entry represents the second Tudor domain of ARID4B. The Tudor domains of these proteins have significantly weaker DNA affinity than that in ARID4A, despite sharing more than 80% sequence identity .

AT-rich interactive domain-containing protein 4B (ARID4B, also known as RBBP1-like 1 (RBBP1L1)) is homologous to ARID4A (or Retinoblastoma-binding protein 1 (RBBP1)) which are involved in cell cycle control . Together with retinoblastoma protein (RB) and Sin3 they form the Sin3 complex involved in gene regulation and epigenetic regulation functions . They also function as transcriptional coactivators for the androgen receptor (AR) and RB, being important for the AR and RB regulatory pathways, involved in the regulation of Sertoli cell function and male fertility . These proteins share the same domain architecture consisting of an interdigitated double Tudor, PWWP, ARID, chromo barrel and R2 domains, connected by intrinsically disordered regions.
Diacylglycerol kinase gamma, second protein kinase C conserved region 1 (C1_DGKgamma_rpt2)
Type: Domain

This entry represents the second protein kinase C conserved region 1 (C1 domain) of DAG kinase gamma and similar proteins from vertebrates. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn2-binding sites.

Diacylglycerol (DAG) kinase (

) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase gamma, also called diglyceride kinase gamma (DGK-gamma), reverses the normal flow of glycerolipid biosynthesis by phosphorylating diacylglycerol back to phosphatidic acid. It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca2 and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DGK-gamma contains two copies of the C1 domain. DGK-gamma contains typical C1 domains that bind DAG and phorbol esters . Through protein kinase C gamma, indirectly regulates the dendritic development of Purkinje cells, cerebellar long term depression and ultimately cerebellar motor coordination .
ARID4B, first Tudor domain (Tudor_ARID4B_rpt1)
Type: Domain

This entry represents the first Tudor domain of ARID4B. The Tudor domains of these proteins have significantly weaker DNA affinity than that in ARID4A, despite sharing more than 80% sequence identity .

AT-rich interactive domain-containing protein 4B (ARID4B, also known as RBBP1-like 1 (RBBP1L1)) is homologous to ARID4A (or Retinoblastoma-binding protein 1 (RBBP1)) which are involved in cell cycle control . Together with retinoblastoma protein (RB) and Sin3 they form the Sin3 complex involved in gene regulation and epigenetic regulation functions . They also function as transcriptional coactivators for the androgen receptor (AR) and RB, being important for the AR and RB regulatory pathways, involved in the regulation of Sertoli cell function and male fertility . These proteins share the same domain architecture consisting of an interdigitated double Tudor, PWWP, ARID, chromo barrel and R2 domains, connected by intrinsically disordered regions.
Diacylglycerol kinase delta, second protein kinase C conserved region 1 (C1_DGKdelta_rpt2)
Type: Domain

This entry represents the second protein kinase C conserved region 1 (C1 domain) of DAG kinase delta and similar proteins mainly found in vertebrates. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn2-binding sites.

Diacylglycerol (DAG) kinase (

) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid.DGK-delta is a member of the diacylglycerol kinase family. DGK-delta is involved in the regulation of clathrin-dependent endocytosis . It is a residential lipid kinase in the endoplasmic reticulum. It promotes lipogenesis and is involved in triglyceride biosynthesis . The SAM domain of DGK-delta proteins can form high molecular weight homooligomers through head-to-tail interactions as well as heterooligomers with the SAM domain of DGK-eta proteins. The oligomerisation plays a role in the regulation of the DGK-delta intracellular localisation: it inhibits the translocation of the protein to the plasma membrane from the cytoplasm . The SAM domain also can bind Zn at multiple (not conserved) sites driving the formation of highly ordered large sheets of polymers, thus suggesting that Zn may play important role in the function of DCK-delta . DAG kinase delta also contains two copies of the C1 domain.
Diacylglycerol kinase delta, first protein kinase C conserved region 1 (C1_DGKdelta_rpt1)
Type: Domain

This entry represents the first protein kinase C conserved region 1 (C1 domain) of DAG kinase delta and similar proteins from vertebrates. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn2-binding sites.

Diacylglycerol (DAG) kinase (

) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid.DGK-delta is a member of the diacylglycerol kinase family. DGK-delta is involved in the regulation of clathrin-dependent endocytosis . It is a residential lipid kinase in the endoplasmic reticulum. It promotes lipogenesis and is involved in triglyceride biosynthesis . The SAM domain of DGK-delta proteins can form high molecular weight homooligomers through head-to-tail interactions as well as heterooligomers with the SAM domain of DGK-eta proteins. The oligomerisation plays a role in the regulation of the DGK-delta intracellular localisation: it inhibits the translocation of the protein to the plasma membrane from the cytoplasm . The SAM domain also can bind Zn at multiple (not conserved) sites driving the formation of highly ordered large sheets of polymers, thus suggesting that Zn may play important role in the function of DCK-delta . DAG kinase delta also contains two copies of the C1 domain.
Lysine-specific demethylase 4A, first Tudor domain (Tudor_KDM4A_rpt1)
Type: Domain

This entry represents the first tudor domain of KDM4A, which is a methyl-lysine reader domain .

Lysine-specific demethylase 4A (KDM4A), also known as JMJD2A or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyses the demethylation of di- and trimethylated histone H3, specifically at 'Lys-9' and 'Lys-36' positions (H3K9 and H3K36) . It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor corepressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER), and plays an essential role in growth of both ER-positive and -negative breast tumours . It is also involved in prostate, colon, and lung cancer progression . JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains .
Diacylglycerol kinase eta, second protein kinase C conserved region 1 (C1_DGKeta_rpt2)
Type: Domain

This entry represents the second protein kinase C conserved region 1 (C1 domain) of DAG kinase eta and similar proteins from vertebrates. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn2-binding sites.

Diacylglycerol (DAG) kinase (

) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase eta, also called diglyceride kinase eta (DGK-eta), plays a key role in promoting cell growth . It is classified as a type II DAG kinase (DGK), containing pleckstrin homology (PH) and sterile alpha motifs (SAM) domains, in addition to C1 and catalytic domains that are present in all DGKs. The SAM domain mediates oligomerization of type II DGKs. The diacylglycerol kinase eta gene, DGKH, is a replicated risk gene of bipolar disorder (BPD) . DAG kinase eta contains two copies of the C1 domain.