8PO8

Structure of Escherichia coli HrpA in complex with ADP and oligonucleotide poly(dC)11 forming an i-motif

Summary for 8PO8

• Entry DOI: 10.2210/pdb8po8/pdb
• Descriptor: ATP-dependent RNA helicase HrpA, DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3'), ADENOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: helicase, hydrolase
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 4
• Total formula weight: 180038.87

Authors

Xin, B.G.,Yuan, L.G.,Zhang, L.L.,Xie, S.M.,Liu, N.N.,Ai, X.,Li, H.H.,Rety, S.,Xi, X.G. (deposition date: 2023-07-03, release date: 2024-05-08)

Primary citation

Xin, B.G.,Huang, L.Y.,Yuan, L.G.,Liu, N.N.,Li, H.H.,Ai, X.,Lei, D.S.,Hou, X.M.,Rety, S.,Xi, X.G.
Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.
Nucleic Acids Res., 52:3406-3418, 2024

PubMed 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.

PubMed: 38412313
DOI: 10.1093/nar/gkae138

Experimental method

X-RAY DIFFRACTION (2.52 Å)