InterPro domain: IPR036710

Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 ) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region, plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) ( IPR000783 ) [ 1 , 2 , 3 , 4 ].

This entry represents the N-terminal domain superfamily of eukaryotic RPB5, which has a core structure consisting of three layers (alpha/beta/alpha) [ 5 ]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [ 5 ]. This module is important for positioning the downstream DNA.

1. Solution structure of the RNA polymerase subunit RPB5 from Methanobacterium thermoautotrophicum. Proc. Natl. Acad. Sci. U.S.A. 97, 6311-5
2. RNA polymerase subunit H features a beta-ribbon motif within a novel fold that is present in archaea and eukaryotes. J. Mol. Biol. 287, 753-60
3. Component H of the DNA-dependent RNA polymerases of Archaea is homologous to a subunit shared by the three eucaryal nuclear RNA polymerases. Proc. Natl. Acad. Sci. U.S.A. 89, 407-10
4. Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target. Proc. Natl. Acad. Sci. U.S.A. 97, 6306-10
5. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288, 640-9