3IVK

Crystal Structure of the Catalytic Core of an RNA Polymerase Ribozyme Complexed with an Antigen Binding Antibody Fragment

Summary for 3IVK

• Entry DOI: 10.2210/pdb3ivk/pdb
• Descriptor: Fab light chain, Fab heavy chain, class I ligase product, ... (7 entities in total)
• Functional Keywords: catalytic rna, protein rna complex, rna polymerase ribozyme, rna hairpin epitope, immune system - rna complex, immune system / rna
• Biological source: Mus musculus; More
• Total number of polymer chains: 6
• Total formula weight: 177521.47

Authors

Koldobskaya, Y.,Duguid, E.M.,Shechner, D.M.,Koide, S.,Kossiakoff, A.A.,Bartel, D.P.,Piccirilli, J.A. (deposition date: 2009-09-01, release date: 2010-03-02, Last modification date: 2024-11-27)

Primary citation

Shechner, D.M.,Grant, R.A.,Bagby, S.C.,Koldobskaya, Y.,Piccirilli, J.A.,Bartel, D.P.
Crystal structure of the catalytic core of an RNA-polymerase ribozyme.
Science, 326:1271-1275, 2009

PubMed 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.

PubMed: 19965478
DOI: 10.1126/science.1174676

Experimental method

X-RAY DIFFRACTION (3.1 Å)