InterPro domain: IPR036643

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 to the prokaryotic RNAP alpha (RpoA) 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 [ 1 ].

The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits ( IPR011263 ), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain ( IPR036603 ), dividing it into two halves [ 2 ]. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.

1. Functional analysis of RNA polymerase II Rpb3 mutants of the fission yeast Schizosaccharomyces pombe. Curr. Genet. 39, 210-21
2. Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Science 281, 262-6