Structural organization of box C/D RNA-guided RNA methyltransferase

Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13808-13. doi: 10.1073/pnas.0905128106. Epub 2009 Aug 5.

Abstract

Box C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2'-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity. Here, we determined the crystal structure of an archaeal C/D RNA-protein complex (RNP) composed of all 3 core proteins and an engineered half-guide RNA at 4 A resolution, as well as 2 protein substructures at higher resolution. The RNP structure reveals that the C-terminal domains of Nop5 in the dimeric complex provide symmetric anchoring sites for 2 L7Ae-associated kink-turn motifs of the C/D RNA. A prominent protrusion in Nop5 seems to be important for guide RNA organization and function and for discriminating the structurally related U4 snRNA. Multiple conformations of the N-terminal domain of Nop5 and its associated fibrillarin in different structures indicate the inherent flexibility of the catalytic module, suggesting that a swinging motion of the catalytic module is part of the enzyme mechanism. We also built a model of a native C/D RNP with substrate and fibrillarin in an active conformation. Our results provide insight into the overall organization and mechanism of action of C/D RNA-guided RNA methyltransferases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Archaeal Proteins / chemistry
  • Base Sequence
  • Carrier Proteins / chemistry*
  • Catalysis
  • Chromosomal Proteins, Non-Histone / chemistry
  • Crystallography, X-Ray / methods
  • Molecular Conformation
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Engineering / methods
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA / chemistry
  • RNA, Archaeal / chemistry
  • tRNA Methyltransferases / chemistry*

Substances

  • Archaeal Proteins
  • Carrier Proteins
  • Chromosomal Proteins, Non-Histone
  • RNA, Archaeal
  • fibrillarin
  • RNA
  • tRNA Methyltransferases

Associated data

  • PDB/3ICX
  • PDB/3ID5
  • PDB/3ID6