7PLI

DEAD-box helicase DbpA bound to single stranded RNA and ADP/BeF3

Summary for 7PLI

• Entry DOI: 10.2210/pdb7pli/pdb
• Descriptor: ATP-dependent RNA helicase DbpA, RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3'), ADENOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: dead-box helicase, rna, ribosome biogenesis, atpase, rna binding protein
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 12
• Total formula weight: 344115.28

Authors

Wurm, J.P. (deposition date: 2021-08-31, release date: 2022-09-07, Last modification date: 2024-01-31)

Primary citation

Wurm, J.P.
Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.
Rna, 29:1339-1354, 2023

PubMed 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.

PubMed: 37221012
DOI: 10.1261/rna.079582.123

Experimental method

X-RAY DIFFRACTION (2.5 Å)