7Y18

Crystal structure of ribosomal ITS2 pre-rRNA processing complex from Saccharomyces cerevisiae

Summary for 7Y18

• Entry DOI: 10.2210/pdb7y18/pdb
• Descriptor: Polynucleotide 5'-hydroxyl-kinase GRC3, Protein LAS1 (3 entities in total)
• Functional Keywords: rna processing, nuclease, rna binding protein
• Biological source: Saccharomyces cerevisiae S288C; More
• Total number of polymer chains: 6
• Total formula weight: 395333.29

Authors

Chen, J.,Liu, L. (deposition date: 2022-06-07, release date: 2023-06-14, Last modification date: 2024-01-17)

Primary citation

Chen, J.,Chen, H.,Li, S.,Lin, X.,Hu, R.,Zhang, K.,Liu, L.
Structural and mechanistic insights into ribosomal ITS2 RNA processing by nuclease-kinase machinery.
Elife, 12:-, 2024

PubMed Abstract: Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a polynucleotide kinase Grc3 assemble into a tetramerase responsible for rRNA maturation. Here, we report the structures of full-length and Las1-Grc3 complexes, and Las1. The Las1-Grc3 structures show that the central coiled-coil domain of Las1 facilitates pre-rRNA binding and cleavage, while the Grc3 C-terminal loop motif directly binds to the HEPN active center of Las1 and regulates pre-rRNA cleavage. Structural comparison between Las1 and Las1-Grc3 complex exhibits that Grc3 binding induces conformational rearrangements of catalytic residues associated with HEPN nuclease activation. Biochemical assays identify that Las1 processes pre-rRNA at the two specific sites (C2 and C2'), which greatly facilitates rRNA maturation. Our structures and specific pre-rRNA cleavage findings provide crucial insights into the mechanism and pathway of pre-rRNA processing in ribosome biosynthesis.

PubMed: 38180340
DOI: 10.7554/eLife.86847

Experimental method

X-RAY DIFFRACTION (3.69 Å)