Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase

Mol Cell. 2009 May 14;34(4):427-39. doi: 10.1016/j.molcel.2009.05.005.


H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. The crystal structures of H/ACA RNP with substrate bound at the active site cleft reveal that the substrate is recruited through sequence-specific pairing with guide RNA and essential protein contacts. Substrate binding leads to a reorganization of a preset pseudouridylation pocket and an adaptive movement of the PUA domain and the lower stem of the H/ACA RNA. Moreover, a thumb loop flips from the Gar1-bound state in the substrate-free RNP structure to tightly associate with the substrate. Mutagenesis and enzyme kinetics analysis suggest a critical role of Gar1 and the thumb in substrate turnover, particularly in product release. Comparison with tRNA Psi55 synthase TruB reveals the structural conservation and adaptation between an RNA-guided and stand-alone pseudouridine synthase and provides insight into the guide-independent activity of Cbf5.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Catalytic Domain
  • Crystallography, X-Ray
  • Intramolecular Transferases / genetics
  • Intramolecular Transferases / metabolism*
  • Macromolecular Substances* / chemistry
  • Macromolecular Substances* / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Nucleic Acid Conformation
  • Protein Conformation*
  • RNA / chemistry*
  • RNA / genetics
  • RNA / metabolism*
  • Ribonucleoproteins, Small Nucleolar / chemistry*
  • Ribonucleoproteins, Small Nucleolar / genetics
  • Ribonucleoproteins, Small Nucleolar / metabolism*


  • Macromolecular Substances
  • Ribonucleoproteins, Small Nucleolar
  • RNA
  • Intramolecular Transferases
  • pseudouridine synthases

Associated data

  • PDB/3HAX
  • PDB/3HAY