Multifaceted Functional Complexity of SARS-CoV-2 Helicase Nsp13 Underlies Its Integrated Motor and Remodeling Activities

SARS-CoV-2 nonstructural protein 13 (Nsp13) is a superfamily 1 helicase essential for viral replication. Although its canonical ATP-dependent unwinding activity is well established, the broader functional repertoire of Nsp13 remains unclear. Here, we show that Nsp13 encodes a high degree of complexity by acting as a tunable nucleic acid remodeler that integrates motor and non-motor activities within a single protein. Nsp13 operates in multiple mechanistically distinct regimes, including a canonical ATP-dependent helicase mode and a Mg²⁺-primed, ATP-independent remodeling state capable of destabilizing short duplexes, hairpins, and G-quadruplexes. Mg²⁺ binding allosterically stabilizes a compact RecA1–RecA2 configuration, priming the enzyme for ATP-independent remodeling. Unwinding polarity is substrate-dependent, with duplexes supporting bidirectional remodeling, whereas G-quadruplexes are preferentially resolved in the 5′→3′ direction. Beyond strand separation, Nsp13 also exhibits robust strand annealing and nucleic acid chaperone activities. Cofactors, substrate topology, and enzyme concentration dynamically regulate these activities. Together, our findings establish Nsp13 as a highly integrated nucleic acid remodeling system and reveal how a single viral helicase switches between motor-driven and remodeling-dominated states to meet the structural demands of replication and transcription.