9W2K

Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2)

Summary for 9W2K

• Entry DOI: 10.2210/pdb9w2k/pdb
• Descriptor: tRNA intron endonuclease, DNA/RNA (5'-R(P*AP*CP*CP*GP*AP*CP*CP*A)-D(P*U)-R(P*AP*GP*CP*U)-3'), RNA (5'-R(P*AP*GP*CP*GP*GP*UP*CP*A)-3'), ... (7 entities in total)
• Functional Keywords: archaea, trna, intron, novel catalytic reaction, splicing, splicing-rna complex, splicing/rna
• Biological source: Candidatus Micrarchaeum acidiphilum ARMAN-2; More
• Total number of polymer chains: 5
• Total formula weight: 100345.69

Authors

Hirata, A. (deposition date: 2025-07-28, release date: 2025-09-10)

Primary citation

Miyata, Y.,Yamagami, R.,Kawamura, T.,Hori, H.,Hirata, A.
Structural basis of substrate diversity and functional evolution of archaeal RNA-splicing endonucleases.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Maturation of transfer RNA molecules often requires removal of intronic sequences by endonucleases that recognize diverse RNA secondary structures. Archaeal splicing endonucleases [versatile RNA-splicing endonucleases (VSENs)] exhibit remarkable substrate versatility, yet the structural basis for this broad specificity has remained unclear. Here, we report the 1.8-Å crystal structure of ARMAN-2, an ϵ2-type VSEN from Candidatus Micrarchaeum acidiphilum, in complex with a synthetic bulge-helix-bulge RNA. The structure reveals that a lineage-specific insertion, the ARMAN-specific loop (ASL), interacts with the bulged region of the RNA and helps to orient the scissile phosphate for catalysis via conserved tyrosine and lysine residues. Functional assays confirmed the essential role of the ASL in substrate binding and cleavage. Structural comparisons with (αβ)2-type Crenarchaeal VSENs, which contain a distinct Crenarchaea-specific loop (CSL), and with a eukaryotic equivalent, the TSEN complex, which harbors a previously uncharacterized eukaryotic-specific loop (ESL), uncovered mechanistic convergence across domains of life. We show that the ESL occupies a position analogous to the ASL and CSL, and likely supports bulge stabilization in long introns. These findings establish a mechanistic model for broad substrate recognition by VSENs and suggest that loop-mediated RNA positioning co-evolved with intron complexity in archaeal and eukaryotic lineages.

PubMed: 40884401
DOI: 10.1093/nar/gkaf845

Experimental method

X-RAY DIFFRACTION (1.798 Å)