SNAP output for PDB entry 1drz [SNAP web server]

PDB-id

1drz; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA binding protein-RNA

Method

X-ray (2.3 Å)

Summary

U1a spliceosomal protein-hepatitis delta virus genomic ribozyme complex

Reference

Ferre-D'Amare AR, Zhou K, Doudna JA (1998): "Crystal structure of a hepatitis delta virus ribozyme." Nature, 395, 567-574. 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.