T7 RNA polymerase – Initiation
The crystal structure of T7 RNA polymer in the initiation configuration (1QLN), showing duplex recognition upstream of position -5, the nontemplate strand dissociating (melting) from the template strand, which is dropping into the active site, where it is bound to a nascent 3-base RNA.
Note that the N-terminal domain (1-260) is the platform on which duplex promoter recognition rests. However, a protein beta hairpin from the C-terminal domain rests on top of that and reads out the sequence of middle major groove of the conserved promoter sequence.
Note that the melted bubble is maintained open by a hydrophobic “intercalating” loop that stacks onto the exposed base pair at position -5. Farther upstream, an Arg-rich loop interacts with the far upstream AT-rich minor groove.
Finally, note that as more RNA is synthesized, while keeping the 3′ end of the RNA in the active site, the RNA–DNA hybrid will have to extend “upstream” (away from the active site). We know that the hybrid duplex grows to about 9 bp before the transition to elongation, but it will crash into the N-terminal domain! This means that the N-terminal domain will rotate and translate (relative to the C-terminal domain), to accommodate the growth of this piston. More on that in the next page in this series (still in development).
Next: Initially transcribing RNA polymerase, with a 7 base transcript.