Conserved Site

DNA-directed RNA polymerase, 30-40kDa subunit, conserved site (IPR001514)

Short name: DNA-dir_RNA_pol_30-40kDasu_CS


DNA-directed RNA polymerases EC: (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [PMID: 3052291]. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [PMID: 10499798]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:

  • RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.
  • RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.
  • RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.
Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.

In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 12 polypeptides. It has been shown [PMID: 12694606, PMID: 2187864, PMID: 8367291, PMID: 12860379] that small subunits of about 30 to 40 kDa found in archebacterial and all three types of eukaryotic polymerases are highly conserved. Subunits known to belong to this family are:

  • Saccharomyces cerevisiae RPC5 subunit (or RPC40) from RNA polymerases I and III.
  • Mammalian RPA40 from RNA polymerase I.
  • S. cerevisiae RPB3 subunit from RNA polymerase II.
  • Schizosaccharomyces pombe rpb3 subunit from RNA polymerase II.
  • Mammalian RPB3 (or RPB33) (gene POLR2C) from RNA polymerase II.
  • Conjugation stage-specific protein cnjC from Tetrahymena thermophila, which may be a stage-specific RNA polymerase subunit.
  • Archaebacterial RNA polymerase subunit D (gene rpoD).

GO terms

Biological Process

GO:0006351 transcription, DNA-templated

Molecular Function

GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE patterns