Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition

RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary str uct ures and organizing ribonucleoprotein comple x es. In our study, w e conducted a systematic analysis of the helicase-related activities of Esc heric hia coli HrpA and presented the str uct ures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP h y droly sis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core pla y s an essential role in unwinding RNA / RNA and RNA / DNA duple x es, the N-terminal e xtension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA / DNA duple x un winding. Import antly, the APHB domain is implicated in binding to non-canonical DNA str uct ures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase comple x. T his research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a f oundation f or further in v estigations into the recognition and functional implications of i-motif DNA str uct ures in various biological processes. Gr aphical abstr act