= RNA polymerase trigger loop
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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 (biology)>.<Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis by Dong Wang and others>[Abstract and Figures 1–2: substrate contacts and alternative loop conformations]{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.<Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis by Dong Wang and others>[Figures 1–2, addition/entry-site nucleotide complexes and trigger-loop positions]{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.
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