9JL3

Cryo-EM structure of DRT2-RT-ncRNA binary complex

Summary for 9JL3

• Entry DOI: 10.2210/pdb9jl3/pdb
• EMDB information: 61577
• Descriptor: Antiviral reverse transcriptase Drt2, nucleic acid, MAGNESIUM ION (3 entities in total)
• Functional Keywords: a complex, antiviral protein
• Biological source: Klebsiella pneumoniae; More
• Total number of polymer chains: 2
• Total formula weight: 141347.82

Authors

Zhang, H.,Zhang, S. (deposition date: 2024-09-17, release date: 2026-04-22)

Primary citation

Liu, Z.,Liao, F.,Wu, W.,Zhang, C.,Yue, C.,Chen, A.,Zhang, S.,Liu, Y.,Liu, B.,Han, J.,Zhang, C.,Wang, X.,Li, X.,Li, Z.,Zhang, H.,Yin, H.
Molecular mechanism of the type 2 defense-associated reverse transcriptase.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Defense-associated reverse transcriptase (DRT) systems play a crucial role in prokaryotic defense mechanisms against phage infections. Among the DRT family, DRT2, DRT3, and DRT9 systems employ protein-noncoding RNA (ncRNA) co-regulatory mechanisms to execute defense functions. Here, we focus on the DRT2 system from Klebsiella pneumoniae, which consists of a reverse transcriptase (RT) and an essential ncRNA component. Using biochemical and structural approaches, we determine the structure of the DRT2 system and reveal detailed interaction modes between the DRT2-RT protein and the ncRNA, especially mediated by specialized anchoring loops and pseudoknot-related structures. The RT protein adopts a conventional "right-hand" fold, while a flexible region of the ncRNA exhibits dynamic conformations, likely serving as the template for reverse transcription. DRT2 mediates reverse transcription through a conserved DDD catalytic triad that coordinates a divalent Mg²⁺ ion. Notably, a short DNA primer-ncRNA duplex is accommodated in a positively charged pocket formed by the thumb and fingers domains, and both interaction analysis and mutagenesis studies confirm that duplex stabilization is essential for activity. Structural comparison and phylogenetic studies of DRT2 and other RT proteins, such as group II introns and UG/Abi RTs, highlight the unique adaptation with a straight extended thumb domain and specialized structures for ncRNA-binding, exemplifying an evolutionary trajectory of RT proteins. In conclusion, our findings expand the understanding of the distinctive characteristics of the DRT2 system and the diversity of prokaryotic antiviral strategies.

PubMed: 41206047
DOI: 10.1093/nar/gkaf1135

Experimental method

ELECTRON MICROSCOPY (3.49 Å)