RNA polymerase, RBP11-like subunit (IPR036603)
Short name: RBP11-like
- DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site (IPR008193)
- DNA-directed RNA polymerase, RBP11-like dimerisation domain (IPR009025)
- DNA-directed RNA polymerase, insert domain (IPR011262)
- DNA-directed RNA polymerase, RpoA/D/Rpb3-type (IPR011263)
- DNA-directed RNA polymerase, alpha subunit (IPR011773)
- DNA-directed RNA polymerase subunit D (Rpo3) (IPR022842)
- DNA-directed RNA polymerase subunit L (Rpo11) (IPR022905)
- DNA-directed RNA polymerases I and III subunit AC19 (IPR033898)
- DNA-directed RNA polymerases I and III subunit AC40 (IPR033901)
- DNA-directed RNA polymerase, insert domain superfamily (IPR036643)
- RNA polymerase RBP11 (IPR037685)
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 [PMID: 11453250]. 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 (IPR011263), the Rpb11-like domain is interrupted by an insert domain (IPR011262). In the prokaryotic RNAP alpha subunit, the Rpb11-like domain and the insert domain form two subregions of the N-terminal domain.
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 [PMID: 11313498, PMID: 12191485] have been shown to share a high degree of sequence and structural similarity to the alpha subunit of bacterial RNAP [PMID: 9657722, PMID: 12000971].