Transitions in DNA polymerase β μs-ms dynamics related to substrate binding and catalysis

DNA polymerase β (pol β) plays a central role in the DNA base excision repair pathway and also serves as an important model polymerase. Dynamic characterization of pol β from methyl-TROSY (13)C-(1)H multiple quantum CPMG relaxation dispersion experiments of Ile and Met sidechains and previous backbone relaxation dispersion measurements, reveals transitions in μs-ms dynamics in response to highly variable substrates. Recognition of a 1-nt-gapped DNA substrate is accompanied by significant backbone and sidechain motion in the lyase domain and the DNA binding subdomain of the polymerase domain, that may help to facilitate binding of the apoenzyme to the segments of the DNA upstream and downstream from the gap. Backbone μs-ms motion largely disappears after formation of the pol β–DNA complex, giving rise to an increase in uncoupled μs-ms sidechain motion throughout the enzyme. Formation of an abortive ternary complex using a non-hydrolyzable dNTP results in sidechain motions that fit to a single exchange process localized to the catalytic subdomain, suggesting that this motion may play a role in catalysis.