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. Author manuscript; available in PMC: 2012 Apr 10.
Published in final edited form as: Biochemistry. 2011 Jul 21;50(32):7002–7014. doi: 10.1021/bi200437q

FIGURE 1.

FIGURE 1

Nucleotide addition and pyrophosphorolysis cycle. Template DNA is shown in black, non-template DNA in blue, RNA in red, incoming nucleotide triphosphate and pyrophosphate in green, and Mg2+ in yellow. One template/nontemplate position is colored orange to illustrate translocation. The EC alternates between pre and posttranslocated states with the RNA 3′ nt in the i or i+1 subsites, prior to NTP binding (step 1). NTPs enter the active site when the EC is posttranslocated (step 2). Catalysis (step 3) requires a rate-limiting conformational change in which the trigger loop folds into the trigger helices (not shown). Release of PPi (step 4) completes the nucleotide addition cycle. Pyrophosphorolysis is the reverse reaction of nucleotide addition. Since catalysis itself is reversible, net pyrophosphorolysis requires that the thermodynamic driving force of PPi conversion to NTP+RNA−1 exceed the conversion of NTP to PPi+RNA+1. Pyrophosphorolysis requires the EC be in the pretranslocated register, but whether PPi binding/release and translocation occur with obligate order is not established.