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:

"
Nucleic acid-binding proteins
".

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 55114: RNA polymerase II subunit Rpb8

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 5 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).
3 P20436 (/IPI) Q19826 (/IPI) Q92399 (/IPI)
DNA-directed 5'-3' RNA polymerase activity GO:0003899
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
2 Q54YW8 (/ISS) Q8I5R8 (/ISS)
RNA polymerase I activity GO:0001054
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase I specific promoter to direct initiation and catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
1 P20436 (/IDA)
Single-stranded DNA binding GO:0003697
Interacting selectively and non-covalently with single-stranded DNA.
1 P52434 (/IDA)
Single-stranded DNA binding GO:0003697
Interacting selectively and non-covalently with single-stranded DNA.
1 Q923G2 (/ISO)

There are 36 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
Transcription from RNA polymerase II promoter GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
3 Q54YW8 (/ISS) Q923G2 (/ISS) Q9VNZ3 (/ISS)
Transcription from RNA polymerase II promoter GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
3 P52434 (/TAS) Q92399 (/TAS) Q923G2 (/TAS)
Transcription from RNA polymerase III promoter GO:0006383
The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
2 P20436 (/TAS) Q92399 (/TAS)
MRNA splicing, via spliceosome GO:0000398
The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
1 P52434 (/TAS)
Transcription-coupled nucleotide-excision repair GO:0006283
The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
1 P52434 (/TAS)
Transcription, DNA-templated GO:0006351
The cellular synthesis of RNA on a template of DNA.
1 P52434 (/TAS)
DNA-templated transcription, initiation GO:0006352
Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
1 Q8I5R8 (/ISS)
Transcription from RNA polymerase I promoter GO:0006360
The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
1 P20436 (/IDA)
Transcription from RNA polymerase I promoter GO:0006360
The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
1 P20436 (/IPI)
Transcription from RNA polymerase I promoter GO:0006360
The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
1 Q54YW8 (/ISS)
Transcription from RNA polymerase I promoter GO:0006360
The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
1 Q92399 (/TAS)
Transcription initiation from RNA polymerase I promoter GO:0006361
Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
1 P52434 (/TAS)
Transcription elongation from RNA polymerase I promoter GO:0006362
The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
1 P52434 (/TAS)
Termination of RNA polymerase I transcription GO:0006363
The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit.
1 P52434 (/TAS)
Transcription from RNA polymerase II promoter GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
1 P52434 (/IDA)
Transcription from RNA polymerase II promoter GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
1 P20436 (/IPI)
Transcription from RNA polymerase II promoter GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
1 Q923G2 (/ISO)
Transcription initiation from RNA polymerase II promoter GO:0006367
Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
1 P52434 (/TAS)
Transcription elongation from RNA polymerase II promoter GO:0006368
The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
1 P52434 (/TAS)
7-methylguanosine mRNA capping GO:0006370
Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
1 P52434 (/TAS)
Transcription from RNA polymerase III promoter GO:0006383
The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
1 P20436 (/IGI)
Transcription from RNA polymerase III promoter GO:0006383
The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
1 P20436 (/IPI)
Transcription from RNA polymerase III promoter GO:0006383
The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
1 Q54YW8 (/ISS)
Transcription elongation from RNA polymerase III promoter GO:0006385
The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase III promoter by the addition of ribonucleotides catalyzed by RNA polymerase III.
1 P20436 (/TAS)
Termination of RNA polymerase III transcription GO:0006386
The process in which transcription by RNA polymerase III is terminated; Pol III has an intrinsic ability to terminate transcription upon incorporation of 4 to 6 contiguous U residues.
1 P20436 (/TAS)
Mitotic G2 DNA damage checkpoint GO:0007095
A mitotic cell cycle checkpoint that detects and negatively regulates progression through the G2/M transition of the cell cycle in response to DNA damage.
1 Q9VNZ3 (/IGI)
Fibroblast growth factor receptor signaling pathway GO:0008543
The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
1 P52434 (/TAS)
RNA metabolic process GO:0016070
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
1 P52434 (/TAS)
Positive regulation of type I interferon production GO:0032481
Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
1 P52434 (/TAS)
Somatic stem cell population maintenance GO:0035019
Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
1 P52434 (/TAS)
Response to drug GO:0042493
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
1 Q59MZ8 (/IMP)
SnRNA transcription from RNA polymerase II promoter GO:0042795
The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
1 P52434 (/TAS)
TRNA transcription from RNA polymerase III promoter GO:0042797
The synthesis of transfer RNA (tRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter.
1 P20436 (/IDA)
Positive regulation of gene expression, epigenetic GO:0045815
Any epigenetic process that activates or increases the rate of gene expression.
1 P52434 (/TAS)
Positive regulation of viral transcription GO:0050434
Any process that activates or increases the frequency, rate or extent of viral transcription.
1 P52434 (/TAS)
Regulation of gene silencing by miRNA GO:0060964
Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
1 P52434 (/TAS)

There are 18 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
DNA-directed RNA polymerase II, core complex GO:0005665
RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
5 O81097 (/IDA) P20436 (/IDA) P52434 (/IDA) Q92399 (/IDA) Q9M1A8 (/IDA)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
3 P20436 (/TAS) P52434 (/TAS) Q923G2 (/TAS)
DNA-directed RNA polymerase II, core complex GO:0005665
RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
3 Q54YW8 (/ISS) Q923G2 (/ISS) Q9VNZ3 (/ISS)
DNA-directed RNA polymerase V complex GO:0000419
RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits.
2 O81097 (/IDA) Q9M1A8 (/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.
2 P52434 (/IDA) Q92399 (/IDA)
DNA-directed RNA polymerase III complex GO:0005666
RNA polymerase III, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces 5S rRNA, tRNAs and some of the small nuclear RNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase I and others of which are also found in RNA polymerases I and II. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
2 P20436 (/IDA) Q92399 (/IDA)
DNA-directed RNA polymerase I complex GO:0005736
RNA polymerase I, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces rRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase III and others of which are also found in RNA polymerases II and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
2 P20436 (/IDA) Q92399 (/IDA)
DNA-directed RNA polymerase IV complex GO:0000418
RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase V, while the largest subunit is found only in RNAP IV complex.
1 Q9M1A8 (/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 Q923G2 (/ISO)
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 Q923G2 (/ISS)
DNA-directed RNA polymerase II, core complex GO:0005665
RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
1 Q923G2 (/ISO)
DNA-directed RNA polymerase III complex GO:0005666
RNA polymerase III, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces 5S rRNA, tRNAs and some of the small nuclear RNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase I and others of which are also found in RNA polymerases I and II. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
1 Q54YW8 (/ISS)
DNA-directed RNA polymerase I complex GO:0005736
RNA polymerase I, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces rRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase III and others of which are also found in RNA polymerases II and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
1 Q54YW8 (/ISS)
Cytosol GO:0005829
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
1 Q92399 (/IDA)
Cytosol GO:0005829
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
1 P52434 (/TAS)
DNA-directed RNA polymerase II, holoenzyme GO:0016591
A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters.
1 Q92399 (/IDA)
Protein-DNA complex GO:0032993
A macromolecular complex containing both protein and DNA molecules.
1 P52434 (/IDA)
Protein-DNA complex GO:0032993
A macromolecular complex containing both protein and DNA molecules.
1 Q923G2 (/ISO)