T7 RNA polymerase – elongation
The crystal structure of an elongating T7 RNA polymerase with an 8 base RNA–DNA hybrid (1MSW). Comparing to the initially transcribing structure, we see that the N-terminal domain has lost its promoter contacts and has undergone a dramatic rotation/refolding. The protein beta hairpin that defined promoter specificity is now under the N-terminal domain, such that promoter specific binding has been abolished. The hydrophobic “intercalating” loop and the Arg-rich loop no longer have any role to play.
The 220° rotation of the N-terminal domain achieves two ends functionally. First, the specificity-conferring beta hairpin which previously sat “on top” of the N-terminal domain, has moved and is now more buried in the protein. Additionally, the “refolding loop,” which previously was exposed and moderately disordered, has moved xxx angstrom and is now part of an RNA exit channel, formed by the rotation.
Note that the stability of the elongation complex arises in large part because of the topological locking of the RNA around the DNADNA template strand. We propose that this minimal locking is what set the size of the RNA–DNA hybrid.