The name of this superfamily has been modified since the most recent official CATH+ release (v4_2_0). At the point of the last release, this superfamily was named:

"
Vaccinia Virus protein VP39
".

Functional Families

Overview of the Structural Clusters (SC) and Functional Families within this CATH Superfamily. Clusters with a representative structure are represented by a filled circle.
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FunFam 135603: cDNA FLJ56738, highly similar to Fibrillarin

Please note: GO annotations are assigned to the full protein sequence rather than individual protein domains. Since a given protein can contain multiple domains, it is possible that some of the annotations below come from additional domains that occur in the same protein, but have been classified elsewhere in CATH.

There are 19 GO terms relating to "molecular function"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Protein binding GO:0005515
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
4 P15646 (/IPI) P22087 (/IPI) P22509 (/IPI) P58032 (/IPI)
Histone-glutamine methyltransferase activity GO:1990259
Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-glutamine = S-adenosyl-L-homocysteine + (histone)-N5-methyl-glutamine.
3 P22232 (/ISS) P22509 (/ISS) P35550 (/ISS)
RNA binding GO:0003723
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
2 P22087 (/IDA) Q94AH9 (/IDA)
SnoRNA binding GO:0030515
Interacting selectively and non-covalently with small nucleolar RNA.
2 Q94AH9 (/ISS) Q9FEF8 (/ISS)
Histone-glutamine methyltransferase activity GO:1990259
Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-glutamine = S-adenosyl-L-homocysteine + (histone)-N5-methyl-glutamine.
2 P15646 (/IDA) P22087 (/IDA)
TFIID-class transcription factor binding GO:0001094
Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
1 P22087 (/IPI)
TFIID-class transcription factor binding GO:0001094
Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
1 P35550 (/ISO)
RNA binding GO:0003723
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
1 P35550 (/ISO)
RNA binding GO:0003723
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
1 P22087 (/TAS)
MRNA binding GO:0003729
Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
1 P35551 (/IPI)
O-methyltransferase activity GO:0008171
Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
1 P15646 (/EXP)
RRNA methyltransferase activity GO:0008649
Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule.
1 P15646 (/IDA)
RRNA methyltransferase activity GO:0008649
Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule.
1 P15646 (/IMP)
RRNA methyltransferase activity GO:0008649
Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule.
1 P35551 (/ISO)
RRNA 2'-O-ribose methylation guide activity GO:0030562
Specifies the site of 2'-O-ribose methylation in an rRNA molecule by base pairing with a short sequence around the target residue.
1 Q38AL4 (/IMP)
ATPase binding GO:0051117
Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
1 P22087 (/IPI)
ATPase binding GO:0051117
Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
1 P35550 (/ISO)
Histone-glutamine methyltransferase activity GO:1990259
Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-glutamine = S-adenosyl-L-homocysteine + (histone)-N5-methyl-glutamine.
1 P15646 (/IMP)
Histone-glutamine methyltransferase activity GO:1990259
Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-glutamine = S-adenosyl-L-homocysteine + (histone)-N5-methyl-glutamine.
1 P35550 (/ISO)

There are 27 GO terms relating to "biological process"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Histone glutamine methylation GO:1990258
The modification of a histone by addition of a methyl group to an glutamine residue.
3 P22232 (/ISS) P22509 (/ISS) P35550 (/ISS)
RRNA processing GO:0006364
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
2 P15646 (/IMP) Q38AL4 (/IMP)
Histone glutamine methylation GO:1990258
The modification of a histone by addition of a methyl group to an glutamine residue.
2 P15646 (/IDA) P22087 (/IDA)
RRNA modification GO:0000154
The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
1 P35551 (/ISO)
RRNA 2'-O-methylation GO:0000451
The addition of a methyl group to the 2'-oxygen atom of a nucleotide residue in an rRNA molecule during ribosome biogenesis.
1 P15646 (/TAS)
Box C/D snoRNA 3'-end processing GO:0000494
Any process involved in forming the mature 3' end of a box C/D snoRNA molecule.
1 P15646 (/IMP)
Box C/D snoRNA 3'-end processing GO:0000494
Any process involved in forming the mature 3' end of a box C/D snoRNA molecule.
1 P35551 (/ISO)
Osteoblast differentiation GO:0001649
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
1 P22087 (/IDA)
Osteoblast differentiation GO:0001649
The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
1 P35550 (/ISO)
Regulation of transcription from RNA polymerase I promoter GO:0006356
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter.
1 P15646 (/IDA)
Regulation of transcription from RNA polymerase I promoter GO:0006356
Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter.
1 P15646 (/IMP)
RRNA processing GO:0006364
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
1 P35551 (/ISO)
RRNA processing GO:0006364
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
1 Q8IM23 (/ISS)
RRNA processing GO:0006364
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
1 P22087 (/TAS)
Cellular response to starvation GO:0009267
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
1 Q9W1V3 (/IEP)
SnoRNA metabolic process GO:0016074
The chemical reactions and pathways involving snoRNA, small nucleolar RNA, any of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
1 P35550 (/IMP)
SnoRNA metabolic process GO:0016074
The chemical reactions and pathways involving snoRNA, small nucleolar RNA, any of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
1 Q55CW0 (/ISS)
RRNA methylation GO:0031167
The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
1 P15646 (/IDA)
RRNA methylation GO:0031167
The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
1 P15646 (/IMP)
RRNA methylation GO:0031167
The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
1 P35551 (/ISO)
RRNA methylation GO:0031167
The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
1 P15646 (/TAS)
SnoRNA processing GO:0043144
Any process involved in the conversion of a primary small nucleolar RNA (snoRNA) transcript into a mature snoRNA.
1 P15646 (/IMP)
Positive regulation of translation GO:0045727
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
1 Q22053 (/IMP)
SnoRNA localization GO:0048254
Any process in which small nucleolar RNA is transported to, or maintained in, a specific location.
1 P22087 (/IMP)
SnoRNA localization GO:0048254
Any process in which small nucleolar RNA is transported to, or maintained in, a specific location.
1 P35550 (/ISO)
Histone glutamine methylation GO:1990258
The modification of a histone by addition of a methyl group to an glutamine residue.
1 P15646 (/IMP)
Histone glutamine methylation GO:1990258
The modification of a histone by addition of a methyl group to an glutamine residue.
1 P35550 (/ISO)

There are 29 GO terms relating to "cellular component"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Nucleolus GO:0005730
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
13 E9QV42 (/IDA) P15646 (/IDA) P22087 (/IDA) P22509 (/IDA) P35550 (/IDA) P35551 (/IDA) Q22053 (/IDA) Q5A0V9 (/IDA) Q7ZTZ4 (/IDA) Q8IM23 (/IDA)
(3 more)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
8 A6NHQ2 (/IDA) M0QXL5 (/IDA) M0R0P1 (/IDA) M0R299 (/IDA) M0R2Q4 (/IDA) P22087 (/IDA) P35551 (/IDA) Q8IM23 (/IDA)
Fibrillar center GO:0001650
A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures.
6 A6NHQ2 (/IDA) M0QXL5 (/IDA) M0R0P1 (/IDA) M0R299 (/IDA) M0R2Q4 (/IDA) P22087 (/IDA)
Nucleolus GO:0005730
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
5 P22232 (/ISS) P22509 (/ISS) P35550 (/ISS) Q55CW0 (/ISS) Q9FEF8 (/ISS)
Cajal body GO:0015030
A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
4 P22087 (/IDA) P22509 (/IDA) P35550 (/IDA) Q9W1V3 (/IDA)
Dense fibrillar component GO:0001651
A structure found in the nucleolus, which contains newly synthesized preribosomal RNA (pre-rRNA) and a collection of proteins.
2 Q8I1F4 (/ISS) Q9W1V3 (/ISS)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
2 P22509 (/IDA) Q22053 (/IDA)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
2 P15646 (/TAS) P22087 (/TAS)
Nucleolus GO:0005730
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
2 P35550 (/ISO) P35551 (/ISO)
Small nucleolar ribonucleoprotein complex GO:0005732
A ribonucleoprotein complex that contains an RNA molecule of the small nucleolar RNA (snoRNA) family and associated proteins. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type.
2 Q8IM23 (/ISS) Q9W1V3 (/ISS)
Membrane GO:0016020
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
2 P22087 (/IDA) Q9FEF8 (/IDA)
Small-subunit processome GO:0032040
A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.
2 P15646 (/IDA) Q5A0V9 (/IDA)
Nuclear chromosome GO:0000228
A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
1 Q5A0V9 (/IDA)
Fibrillar center GO:0001650
A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures.
1 P35550 (/ISO)
Dense fibrillar component GO:0001651
A structure found in the nucleolus, which contains newly synthesized preribosomal RNA (pre-rRNA) and a collection of proteins.
1 P22509 (/IDA)
Granular component GO:0001652
A structure found in the nucleolus, which contains nearly completed preribosomal particles destined for the cytoplasm.
1 P35550 (/IDA)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
1 P35550 (/ISO)
Chromosome GO:0005694
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
1 P22509 (/IDA)
Cajal body GO:0015030
A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
1 P35550 (/ISO)
Membrane GO:0016020
A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
1 P35550 (/ISO)
Mediator complex GO:0016592
A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
1 Q94AH9 (/IDA)
Small nuclear ribonucleoprotein complex GO:0030532
A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs.
1 Q9W1V3 (/ISS)
Box C/D snoRNP complex GO:0031428
A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs.
1 P15646 (/IDA)
Box C/D snoRNP complex GO:0031428
A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs.
1 Q38AL4 (/IMP)
Box C/D snoRNP complex GO:0031428
A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs.
1 P22087 (/NAS)
Small-subunit processome GO:0032040
A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.
1 P35551 (/ISO)
Extracellular exosome GO:0070062
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
1 P22087 (/IDA)
Extracellular exosome GO:0070062
A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
1 P35550 (/ISO)
Mitotic spindle GO:0072686
A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
1 P35551 (/IDA)
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