Active center rearrangement in RNA polymerase initiation complex.

His1237 in the beta subunit of Escherichia coli RNA polymerase marks the "5' face" of the active center since it can be cross-linked to the gamma-phosphate of the priming substrate. It is demonstrated that RNA chains up to 9 nucleotides in length can be synthesized using His1237-cross-linked nucleotide as a primer. Thus, a substantial mass of RNA can be accommodated in the active center between His1237 and the site of catalysis that remains juxtaposed to the growing 3' end. The apparent "filling" of the active center with RNA precedes promoter clearance and suggests a mechanism of coupling between catalysis and saltatory translocation of RNA polymerase.