 RNA polymerase trigger loop

The RNA polymerase trigger loop is a mobile protein element near the active site of multisubunit RNA polymerase. In RNA polymerase II, it can close beneath a correctly positioned incoming nucleoside triphosphate and form contacts with its base, sugar and phosphate groups. Its movement links recognition of the substrate with efficient phosphodiester bond formation during transcription.^[ref]

The 2006 structural study compared transcribing complexes with different bound nucleotides. A correct substrate in the addition site was associated with a closed conformation and an extensive interaction network. This gave a physical explanation for why merely entering the active-site region is not sufficient for efficient incorporation: the substrate must also support a productive arrangement of the surrounding polymerase.^[ref]

For an illuminating comparison, imagine two nucleotides that bind detectably but support loop closure with different probabilities. Equal binding abundance would not imply equal incorporation rates, because productive positioning contributes a further step. This is a schematic kinetic argument, not a measurement of a particular pair of rate constants.

The adjacent RNA polymerase bridge helix and the RNA polymerase trigger loop are distinct structural elements. A proposed catalytic role for a loop residue must also be distinguished from what is directly observed in a crystal: geometry can suggest a chemical mechanism, while mutagenesis and kinetics test its consequences.