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 [1]. 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 [2, 3] have been shown to share a high degree of sequence and structural similarity to the alpha subunit of bacterial RNAP [4, 5].

1. Functional analysis of RNA polymerase II Rpb3 mutants of the fission yeast Schizosaccharomyces pombe. Curr. Genet. 39, 210-21
2. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863-76
3. Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol. Cell 10, 409-15
4. Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Science 281, 262-6
5. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417, 712-9

RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of
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