Crystal structure of a hepatitis delta virus ribozyme

Nature. 1998 Oct 8;395(6702):567-74. doi: 10.1038/26912.

Abstract

The self-cleaving ribozyme of the hepatitis delta virus (HDV) is the only catalytic RNA known to be required for the viability of a human pathogen. We obtained crystals of a 72-nucleotide, self-cleaved form of the genomic HDV ribozyme that diffract X-rays to 2.3 A resolution by engineering the RNA to bind a small, basic protein without affecting ribozyme activity. The co-crystal structure shows that the compact catalytic core comprises five helical segments connected as an intricate nested double pseudoknot. The 5'-hydroxyl leaving group resulting from the self-scission reaction is buried deep within an active-site cleft produced by juxtaposition of the helices and five strand-crossovers, and is surrounded by biochemically important backbone and base functional groups in a manner reminiscent of protein enzymes.

Publication types

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

MeSH terms

  • Base Sequence
  • Binding Sites
  • Catalysis
  • Cloning, Molecular
  • Computer Graphics
  • Crystallography, X-Ray
  • Escherichia coli
  • Hepatitis Delta Virus / enzymology
  • Hepatitis Delta Virus / genetics*
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • RNA, Catalytic / chemistry*
  • RNA, Viral / chemistry*
  • RNA-Binding Proteins*
  • Ribonucleoprotein, U1 Small Nuclear / chemistry

Substances

  • RNA, Catalytic
  • RNA, Viral
  • RNA-Binding Proteins
  • Ribonucleoprotein, U1 Small Nuclear
  • U1A protein

Associated data

  • PDB/1DRZ