SNAP output for PDB entry 7pmq [SNAP web server]

PDB-id

7pmq; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA binding protein

Method

X-ray (3.22 Å)

Summary

Dead-box helicase dbpa in the active conformation bound to a hairpin loop RNA and adp-bef3

Reference

Wurm JP (2023): "Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA." Rna, 29, 1339-1354. doi: 10.1261/rna.079582.123.

Abstract

DEAD-box RNA helicases are implicated in most aspects of RNA biology, where these enzymes unwind short RNA duplexes in an ATP-dependent manner. During the central step of the unwinding cycle, the two domains of the helicase core form a distinct closed conformation that destabilizes the RNA duplex, which ultimately leads to duplex melting. Despite the importance of this step for the unwinding process no high-resolution structures of this state are available. Here, I used nuclear magnetic resonance spectroscopy and X-ray crystallography to determine structures of the DEAD-box helicase DbpA in the closed conformation, complexed with substrate duplexes and single-stranded unwinding product. These structures reveal that DbpA initiates duplex unwinding by interacting with up to three base-paired nucleotides and a 5' single-stranded RNA duplex overhang. These high-resolution snapshots, together with biochemical assays, rationalize the destabilization of the RNA duplex and are integrated into a conclusive model of the unwinding process.