T7 RNA polymerase structure exploration
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The crystal structure of T7 RNA polymerase in the initiation configuration (1QLN), showing duplex recognition upstream of position -5, the dissociating (melting) from the , which is dropping into the active site, where it is bound to a . [Reset view]
Note that the (1-260) is the platform on which duplex promoter recognition rests. However, a 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 that stacks onto the exposed base pair at . Farther upstream, an interacts with the far upstream AT-rich minor groove. 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 will rotate and translate (relative to the C-terminal domain), to accommodate the growth of this piston. This rotation moves “” from a very solvent exposed position into a new position where it contributes to the RNA exit channel. More on that in the next page in this series (still in development).
Finally, note the is positioned near the 3′ end of the nascent RNA.