The RNA polymerase bridge helix is an alpha helix spanning the active site region of RNA polymerase. In RNA polymerase II, it lies near the template DNA and growing RNA, where conformational changes can alter the space available for template positioning during transcription.[ref]
Researchers soaked transcription elongation complex crystals with alpha-amanitin. The trapped structure showed the entering DNA base above a shifted RNA polymerase bridge helix, with the usual templating position obstructed. The authors interpreted the arrangement as a possible intermediate in movement along DNA.[ref]
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation by Florian Brueckner and Patrick Cramer. Abstract: inhibitor soaking and proposed translocation intermediate
The useful connection is between local protein geometry and which DNA base can be presented to the catalytic machinery. Successive addition cycles require that relationship to change while sequence order remains intact. A trapped conformation is evidence about an accessible arrangement; establishing its timing and contribution to normal movement also requires kinetic measurements. The helix is part of the coupled enzyme, rather than an independently operating motor.
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