SNAP output for PDB entry 8po7 [SNAP web server]

PDB-id

8po7; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase

Method

X-ray (2.26 Å)

Summary

Structure of escherichia coli hrpa in complex with adp and dinucleotide dcdc

Reference

Xin BG, Huang LY, Yuan LG, Liu NN, Li HH, Ai X, Lei DS, Hou XM, Rety S, Xi XG (2024): "Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition." Nucleic Acids Res., 52, 3406-3418. doi: 10.1093/nar/gkae138.

Abstract

RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary structures and organizing ribonucleoprotein complexes. In our study, we conducted a systematic analysis of the helicase-related activities of Escherichia coli HrpA and presented the structures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP hydrolysis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core plays an essential role in unwinding RNA/RNA and RNA/DNA duplexes, the N-terminal extension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA/DNA duplex unwinding. Importantly, the APHB domain is implicated in binding to non-canonical DNA structures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase complex. This research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a foundation for further investigations into the recognition and functional implications of i-motif DNA structures in various biological processes.