Subunits

The eukaryotic form of the enzyme has 12 subunits labeled RPB1 through RPB 12. Roger Kornberg and colleagues performed a multi-step purification of the enzyme followed by SDS PAGE analysis to distinguish all subunits (Weaver 1999). The structures are further classified as core subunits, common subunits, and nonessential subunits. The three largest subunits, RPB1, RPB2, and RPB3 constitute the structural and functional core of the enzyme (Weaver 1999). RPB1 and RPB2 are functionally comparable to b and b' of the E. coli RNA polymerase. RPB3 has been proposed to be analogous to the a-subunit of the E. coli polymerase. Subunits RPB5, RPB6, RPB8, RPB10, and RPB12 are denoted common subunits as they are shared by RNA polymerases I and III. This correlation was evidenced by identical gel mobility using electrophoresis. These subunits interact with multiple accessory proteins called general transcription factors.

Picture of RNA Polymerase II with the subunits (RPB 1-12), Adopted from ALS Science

RNA polymerases with mutant subunits RPB4 and RPB9 have determined that these subunits are non-essential for transcription under normal conditions. Interactions between the subunits, as well as, their individual study are the current focus of research. Through cross-linking, the "use of five species of bifunctional cross linkers of various length were inserted between the two reactive sites and in the target amino acid residues for conjugation" and far-Western blotting, direct interactions between the subunits has been determined (Ishiguro 1998). Research demonstrates the cross-linking of RPB 1 with 3,5,6,8, 11, and 12. Similarly, cross-linking of RPB2 with 3,5,6,7,10,11, and 12 was demonstrated.

These data further supports the classification of RPB1 and RPB2 as core subunits essentially providing the structure for the polymerase development (Ishiguro 1998). The primary method of determining protein function has been to purify the associated gene, mutate, and perform experiments to make conclusions regarding viability and efficiency of binding and elongation.