The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain

BACKGROUND: Cellular RNA polymerases (RNAPs) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-H(C)) plays a critical role in controlling the catalytic rate. RESULTS: Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-H(N)) is presented. The nanomechanical properties of BH-H(N )emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC). BH-H(N )displays functional properties that are distinct from BH-H(C), suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. CONCLUSIONS: The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.