During gene transcription, the RNA polymerase (Pol) active center can catalyze 
RNA cleavage. This intrinsic cleavage activity is strong for Pol I and Pol III 
but very weak for Pol II. The reason for this difference is unclear because the 
active centers of the polymerases are virtually identical. Here we show that Pol 
II gains strong cleavage activity when the C-terminal zinc ribbon domain 
(C-ribbon) of subunit Rpb9 is replaced by its counterpart from the Pol III 
subunit C11. X-ray analysis shows that the C-ribbon has detached from its site 
on the Pol II surface and is mobile. Mutagenesis indicates that the C-ribbon 
transiently inserts into the Pol II pore to complement the active center. This 
mechanism is also used by transcription factor IIS, a factor that can bind Pol 
II and induce strong RNA cleavage. Together with published data, our results 
indicate that Pol I and Pol III contain catalytic C-ribbons that complement the 
active center, whereas Pol II contains a non-catalytic C-ribbon that is 
immobilized on the enzyme surface. Evolution of the Pol II system may have 
rendered mRNA transcript cleavage controllable by the dissociable factor 
transcription factor IIS to enable promoter-proximal gene regulation and 
elaborate 3'-processing and transcription termination.