The team traced that protein density back to a portion of the polymerase II enzyme: the trigger loop.
“Of the 14 crystal structures now reported in which the trigger loop was observed, only in two is it seen in that location, directly beneath the NTP,?Kornberg said. Those were the only two crystals in which the NTP was correctly matched to the DNA template, evidence of the trigger loop’s “clear relationship to NTP selection.?
Further study revealed that, when a matching NTP reaches the addition site, the trigger loop swings from its usual position some distance away until it rests parallel to the NTP. It then forms a network of interactions—some 20 to 30 in all—with components of the NTP, a process that serves to “recognize all features of the NTP in the addition site and detect its precise location,?the researchers reported.
“The specificity is a result of the alignment with the NTP that is critically dependent upon the base, sugar, phosphate and location when the trigger loop swings into position,?Kornberg said. “If it is misaligned even slightly, that set of contacts cannot occur.?
As a consequence of that alignment, to angstrom (a unit of length equal to one hundred millionth of a centimeter) precision, a histidine side chain of the trigger loop rests on the ß phosphate, the chemical constituent that must have its bond broken in order for the NTP to join the RNA chain through the formation of a phosphodiester bond, Kornberg said. The finding suggested the side chain acts as a trigger for bond formation.
The whole decision-making process occurs extremely rapidly, he added, on the order of picoseconds. A picosecond is one trillionth of a second.
“The basis for the extraordinary specificity with which RNA polymerases transcribe DNA lies in a structural element termed the trigger loop, which makes both direct and indirect contact with all features of the nucleotide in the polymer