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Figure 6.
Fig. 6. Proposed transcription cycle and translocation
mechanism. (A) Schematic representation of the nucleotide
addition cycle. The nucleotide triphosphate (NTP) fills the open
substrate site (top) and forms a phosphodiester bond at the
active site ("Synthesis"). This results in the state of the
transcribing complex seen in the crystal structure (middle). We
speculate that "Translocation" of the nucleic acids with respect
to the active site (marked by a pink dot for metal A) involves a
change of the bridge helix from a straight (silver circle) to a
bent conformation (violet circle, bottom). Relaxation of the
bridge helix back to a straight conformation without movement of
the nucleic acids would result in an open substrate site one
nucleotide downstream and would complete the cycle. (B)
Different conformations of the bridge helix in pol II and
bacterial RNA polymerase structures. The view is the same as in
Fig. 2C. The bacterial RNA polymerase structure (2) was
superimposed on the pol II transcribing complex by fitting
residues around the active site. The resulting fit of the bridge
helices of pol II (silver) and the bacterial polymerase (violet)
is shown. The bend in the bridge helix in the bacterial
polymerase structure causes a clash of amino acid side chains
(extending from the backbone shown here) with the hybrid base
pair at position +1.
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