PDBsum entry 1vby

Translation/RNA

PDB id: 1vby

Contents

Protein chain

95 a.a. *

DNA/RNA

Metals

_NA

_MN ×2

Waters ×14

* Residue conservation analysis

References listed in PDB file

Key reference

Title

A conformational switch controls hepatitis delta virus ribozyme catalysis.

Authors

A.Ke, K.Zhou, F.Ding, J.H.Cate, J.A.Doudna.

Ref.

Nature, 2004, 429, 201-205. [DOI no: 10.1038/nature02522]

PubMed id

15141216

Abstract

Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.

Figure 2.
Figure 2: Conformational changes in the active site accompany HDV ribozyme cleavage. a, 3.4 Å experimental electron-density map of the wild-type precursor HDV ribozyme (1 ) superimposed on the refined wild-type structure model (magenta) and that of the C75U mutant (grey). b, Backbone alignment of the precursor (magenta) and product (grey) ribozyme structures. c, Stereo view of the aligned active sites of the precursor (coloured) and product (grey) ribozyme structures. Conformational changes were modelled using the C75U mutant ribozyme structure, shown by arrows.

Figure 3.
Figure 3: Proposed mechanism for general acid -base catalysis in the HDV ribozyme. a, In the ground state, a hinge rotation along O3'-P bond brings the nucleophilic 2'-OH to the in-line attack conformation. In the transition state, C75 (the general base) deprotonates the 2'-OH whereas the bound hydrated metal ion (the general acid) protonates the 5' oxygen leaving group. Conformational changes after scissile bond breakage discharge the catalytic metal ion and down-shift the catalytic base C75 by 2 Å to enable hydrogen bonding with the 5'-OH of G1. b, Structural models of the HDV ribozyme in the ground state, transition state and product state. Some metal-chelating groups and coordinating waters are omitted for clarity.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2004, 429, 201-205) copyright 2004.