Standard preparations of Escherichia coli RNA polymerase (RNAP) contain NTPase activity. High-performance anion-exchange chromatography on Mono Q has recently been used by Hager et al. [1990, Biochemistry 29, 7890-7894] to fractionate RNAP into holoenzyme (alpha 2 beta beta' sigma) and core (alpha 2 beta beta') forms, plus other protein components. We found that one of these components, of protomer size slightly larger than the sigma 70 subunit, has NTPase activity; it is efficiently separated on Mono Q, leaving transcriptionally active holoenzyme and core apparently free of NTPase activity. Because of the similarity in size with sigma 70, the NTPase component may escape detection by routine gel electrophoresis.
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