SNAP output for PDB entry 3ivk [SNAP web server]

PDB-id

3ivk; SNAP-derived features in text and JSON formats; DNAproDB

Class

immune system - RNA

Method

X-ray (3.1 Å)

Summary

Crystal structure of the catalytic core of an RNA polymerase ribozyme complexed with an antigen binding antibody fragment

Reference

Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP (2009): "Crystal structure of the catalytic core of an RNA-polymerase ribozyme." Science, 326, 1271-1275. doi: 10.1126/science.1174676.

Abstract

Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best approximating that needed for RNA replication contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate among the fastest of known ribozymes. Here we present the 3.0 angstrom crystal structure of this ligase. The architecture resembles a tripod, its three legs converging near the ligation junction. Interacting with this tripod scaffold through a series of 10 minor-groove interactions (including two A-minor triads) is the unpaired segment that contributes to and organizes the active site. A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases.