9w2k

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

spinqualitylabelsall models 9w2k, resolution 1.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9w2k is a 5 chain structure with sequence from Archaeoglobus fulgidus and Candidatus Micrarchaeum acidiphilum ARMAN-2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.798Å Ligands: A23, ACY Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function C7DIA5_MICA2 Publication Abstract from PubMed 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-A 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 (alphabeta)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. Structural basis of substrate diversity and functional evolution of archaeal RNA-splicing endonucleases.,Miyata Y, Yamagami R, Kawamura T, Hori H, Hirata A Nucleic Acids Res. 2025 Aug 27;53(16):gkaf845. doi: 10.1093/nar/gkaf845. PMID:40884401 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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