<p>DNA-directed RNA polymerases <db_xref db="EC" dbkey="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 multimericenzymes 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 [<cite idref="PUB00000061"/>]. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [<cite idref="PUB00033173"/>]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.</p><p>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: <ul> <li>RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.</li> <li>RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. </li> <li>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. </li> </ul>Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular massesvary 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.</p><p>RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and the prokaryotic RNAP alpha subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact [<cite idref="PUB00013987"/>]. These different subunits share regions of homology. Rpb11 contains a domain (Rpb11-like domain) that is required for dimerisation, and binds to a homologous region on Rpb3. The Rpb11-like domain in Rpb11 and archaeal L subunits is contiguous, whereas in Rpb3, archaeal D, and prokaryotic alpha subunits (<db_xref db="INTERPRO" dbkey="IPR011263"/>), the Rpb11-like domain is interrupted by an insert domain (<db_xref db="INTERPRO" dbkey="IPR011262"/>). In the prokaryotic RNAP alpha subunit, the Rpb11-like domain and the insert domain form two subregions of the N-terminal domain.</p><p>The structure of the Rpb11-like domain consists of a two-layer alpha/beta fold consisting of beta(2)-alpha-beta(2)-alpha. Rpb3 and Rpb11 in yeast RNAP [<cite idref="PUB00008731"/>, <cite idref="PUB00013986"/>] have been shown to share a high degree of sequence and structural similarity to the alpha subunit of bacterial RNAP [<cite idref="PUB00005231"/>, <cite idref="PUB00011749"/>].</p>
DNA-directed RNA polymerase, RBP11-like