8J60

Structural and mechanistic insight into ribosomal ITS2 RNA processing by nuclease-kinase machinery

Summary for 8J60

• Entry DOI: 10.2210/pdb8j60/pdb
• EMDB information: 33735
• Descriptor: Polynucleotide 5'-hydroxyl-kinase GRC3, LAS1 protein (2 entities in total)
• Functional Keywords: endoribonuclease; ribosome biosynthesis; las1; grc3, rna binding protein
• Biological source: Cyberlindnera jadinii; More
• Total number of polymer chains: 4
• Total formula weight: 238052.98

Authors

Chen, J.,Chen, H.,Li, S.,Lin, X.,Hu, R.,Zhang, K.,Liu, L. (deposition date: 2023-04-24, release date: 2024-01-17, Last modification date: 2024-10-16)

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

ELECTRON MICROSCOPY (3.39 Å)