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TitleStructural and mechanistic insights into ribosomal ITS2 RNA processing by nuclease-kinase machinery.
Journal, issue, pagesElife, Vol. 12, Year 2024
Publish dateJan 5, 2024
AuthorsJiyun Chen / Hong Chen / Shanshan Li / Xiaofeng Lin / Rong Hu / Kaiming Zhang / Liang Liu /
PubMed AbstractPrecursor 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 ...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.
External linksElife / PubMed:38180340 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.8 - 3.69 Å
Structure data

33733

8j5y

EMDB-33733: Cryo-EM structure of ScLas1-Grc3 complex
PDB-8j5y: Structural and mechanistic insight into ribosomal ITS2 RNA processing by nuclease-kinase machinery
Method: EM (single particle) / Resolution: 3.07 Å

33735

8j60

EMDB-33735: Cryo-EM structure of CjLas1-Grc3 complex
PDB-8j60: Structural and mechanistic insight into ribosomal ITS2 RNA processing by nuclease-kinase machinery
Method: EM (single particle) / Resolution: 3.39 Å

PDB-7y16:
Crystal structure of rRNA-processing protein Las1
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7y17:
Crystal structure of ribosomal ITS2 pre-rRNA processing complex from Cyberlindnera jadinii
Method: X-RAY DIFFRACTION / Resolution: 3.39 Å

PDB-7y18:
Crystal structure of ribosomal ITS2 pre-rRNA processing complex from Saccharomyces cerevisiae
Method: X-RAY DIFFRACTION / Resolution: 3.69 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • cyberlindnera jadinii (fungus)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsRNA BINDING PROTEIN / RNA processing / Nuclease / endoribonuclease; ribosome biosynthesis; Las1; Grc3

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