InterPro: IPR008193 DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site

DNA-directed RNA polymerases EC:2.7.7.6 (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 [1]. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [2]. 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.

In archaea, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 12 polypeptides. Small subunits of about 13 to 16 kDa are found in all three types of eukaryotic polymerases and in archaeal polymerase. Subunits that belong to this family include: Rpb11 subunit from RNA polymerase II in eukaryotes [3, 4], subunit L from archaeal RNA polymerase [5] and subunit Rpc19 from RNA polymerases I and II in Saccharomyces cerevisiae (Baker's yeast) [6].