The name of this superfamily has been modified since the most recent official CATH+ release (v4_3_0). At the point of the last release, this superfamily was named:

"
RNA polymerase II, clamp domain
".

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 3: DNA-directed RNA polymerase subunit

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 4 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).
9 O77375 (/IPI) O77375 (/IPI) P04050 (/IPI) P04050 (/IPI) P04050 (/IPI) P04050 (/IPI) P18616 (/IPI) P18616 (/IPI) P36594 (/IPI)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
5 P04050 (/IDA) P04050 (/IDA) P04050 (/IDA) P04050 (/IDA) P36594 (/IDA)
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'.
5 O77375 (/ISS) O77375 (/ISS) P18616 (/ISS) P18616 (/ISS) P35084 (/ISS)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
2 P18616 (/ISS) P18616 (/ISS)

There are 9 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
MRNA trans splicing, SL addition GO:0045291
The joining together of two independently transcribed RNAs, where the one that provides the 5' portion of the final mRNA is from a splice leader RNA (SL-RNA). The SL-RNA, or mini-exon donor sequence, is added to the 5'-end of the acceptor RNA molecule which provides the mRNA body.
5 Q26791 (/IGI) Q26791 (/IGI) Q26791 (/IGI) Q584K3 (/IGI) Q584K3 (/IGI)
Transcription by RNA polymerase II GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
4 P04050 (/IMP) P04050 (/IMP) P04050 (/IMP) P04050 (/IMP)
Translesion synthesis GO:0019985
The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
4 P04050 (/IMP) P04050 (/IMP) P04050 (/IMP) P04050 (/IMP)
Transcription by RNA polymerase II GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
2 O77375 (/ISS) O77375 (/ISS)
Transcription by RNA polymerase II GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
1 P36594 (/EXP)
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 A0A1D8PUA6 (/IMP)
Filamentous growth GO:0030447
The process in which a multicellular organism, a unicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape.
1 A0A1D8PUA6 (/IMP)
Filamentous growth of a population of unicellular organisms in response to starvation GO:0036170
The process in which a group of unicellular organisms grow in a threadlike, filamentous shape in response to deprivation of nourishment.
1 A0A1D8PUA6 (/IMP)
Filamentous growth of a population of unicellular organisms in response to biotic stimulus GO:0036180
The process in which a group of unicellular organisms grow in a threadlike, filamentous shape in response to a biotic (living) stimulus.
1 A0A1D8PUA6 (/IMP)

There are 14 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
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.
7 P04050 (/IDA) P04050 (/IDA) P04050 (/IDA) P04050 (/IDA) P18616 (/IDA) P18616 (/IDA) P36594 (/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.
6 P04050 (/IDA) P04050 (/IDA) P04050 (/IDA) P04050 (/IDA) P35084 (/IDA) Q57YU2 (/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.
5 P04050 (/HDA) P04050 (/HDA) P04050 (/HDA) P04050 (/HDA) P36594 (/HDA)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
5 Q26791 (/IDA) Q26791 (/IDA) Q26791 (/IDA) Q584K3 (/IDA) Q584K3 (/IDA)
Mitochondrion GO:0005739
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
4 P04050 (/HDA) P04050 (/HDA) P04050 (/HDA) P04050 (/HDA)
Cytoplasmic stress granule GO:0010494
A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
4 P04050 (/IDA) P04050 (/IDA) P04050 (/IDA) P04050 (/IDA)
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 O77375 (/ISS) O77375 (/ISS) P35084 (/ISS)
Vacuole GO:0005773
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
2 P18616 (/IDA) P18616 (/IDA)
Plasmodesma GO:0009506
A fine cytoplasmic channel, found in all higher plants, that connects the cytoplasm of one cell to that of an adjacent cell.
2 P18616 (/IDA) P18616 (/IDA)
Chloroplast GO:0009507
A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
2 P18616 (/IDA) P18616 (/IDA)
Nuclear chromatin GO:0000790
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
1 P36594 (/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 Q57YU2 (/TAS)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
1 Q4Q600 (/ISO)
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 P36594 (/HDA)
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