Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle

Mol Cell. 2010 Sep 24;39(6):939-49. doi: 10.1016/j.molcel.2010.08.022.

Abstract

Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Archaeal Proteins / chemistry
  • Archaeal Proteins / genetics
  • Binding Sites / physiology
  • Biocatalysis
  • Chromosomal Proteins, Non-Histone / chemistry
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • Crystallography, X-Ray
  • Holoenzymes / chemistry
  • Holoenzymes / genetics
  • Holoenzymes / metabolism
  • Methyltransferases / chemistry
  • Methyltransferases / genetics
  • Methyltransferases / metabolism
  • Models, Molecular*
  • Mutagenesis, Insertional / physiology
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / genetics
  • Nucleic Acid Conformation
  • Protein Multimerization / physiology
  • Protein Structure, Quaternary / physiology
  • Pyrococcus furiosus / enzymology*
  • Pyrococcus furiosus / genetics
  • RNA, Archaeal / chemistry
  • RNA, Archaeal / metabolism
  • RNA, Small Nucleolar / chemistry
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Ribonucleoproteins, Small Nucleolar / chemistry*
  • Ribonucleoproteins, Small Nucleolar / genetics
  • Ribonucleoproteins, Small Nucleolar / metabolism
  • Sequence Deletion / physiology

Substances

  • Archaeal Proteins
  • Chromosomal Proteins, Non-Histone
  • Holoenzymes
  • Nuclear Proteins
  • RNA, Archaeal
  • RNA, Small Nucleolar
  • Recombinant Proteins
  • Ribonucleoproteins, Small Nucleolar
  • fibrillarin
  • Methyltransferases
  • RNA 2'-O-methyltransferase

Associated data

  • PDB/3NMU
  • PDB/3NVI
  • PDB/3NVK
  • PDB/3NVM