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PDBsum entry 3fs0

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dna_rna metals links
RNA PDB id
3fs0
Jmol
Contents
DNA/RNA
Metals
_MG ×5
Waters ×12
PDB id:
3fs0
Name: RNA
Title: Class ii ligase ribozyme product-template duplex, structure 2
Structure: 5'-r( Gp Gp Up Gp Ap Gp Gp Cp Up G)-3'. Chain: a. Engineered: yes. Other_details: template strand of class ii ligase a4-11. 5'-r( Cp Cp Ap Gp Up Cp Gp Gp Ap Ap C)-3'. Chain: b. Engineered: yes. Other_details: product strand of class ii ligase a4-11, single stranded RNA with one 2'-5' linkage
Source: Synthetic: yes. Synthetic: yes
Resolution:
2.30Å     R-factor:   0.208     R-free:   0.234
Authors: J.N.Pitt,A.R.Ferre-D'Amare
Key ref: J.N.Pitt and A.R.Ferré-D'Amaré (2009). Structure-guided engineering of the regioselectivity of RNA ligase ribozymes. J Am Chem Soc, 131, 3532-3540. PubMed id: 19220054
Date:
08-Jan-09     Release date:   24-Feb-09    
 Headers
 References

 

 
J Am Chem Soc 131:3532-3540 (2009)
PubMed id: 19220054  
 
 
Structure-guided engineering of the regioselectivity of RNA ligase ribozymes.
J.N.Pitt, A.R.Ferré-D'Amaré.
 
  ABSTRACT  
 
Ribozyme-catalyzed RNA synthesis is central to the RNA world hypothesis. No natural RNA polymerase ribozymes have been discovered. However, ribozymes that catalyze the requisite chemistry, generating a new phosphodiester through attack of a terminal hydroxyl of an RNA on the alpha-phosphate of a triphosphate-activated oligonucleotide, have been isolated by in vitro selection. These experiments often yield ribozymes that generate 2'-5' phosphodiesters rather than conventional 3'-5' linkages. We have determined crystal structures of the duplex formed by the template segment of a representative 2'-5' RNA ligase ribozyme, the class II ligase, and its ligation product. The structures reveal a product-template duplex with a G x A pair at the ligation junction. This sheared pair is flanked on one side by a minor groove-broadening wedge comprised of two unpaired nucleotides. The reported structure of an independently isolated 3'-5' ligase ribozyme, the L1 ligase, shows a product-template duplex that shares the G x A pair with the class II ligase. However, this G x A pair is flanked by G x U wobbles, rather than an unpaired wedge. We demonstrate that these structural differences of the substrate-template duplexes are largely responsible for the divergent regioselectivity of the two ribozymes, independent of their catalytic moieties, by constructing chimeras. The L1 ligase with a class II substrate-template duplex shows a 30-fold increase in 2'-5' bond synthesis, while the class II ligase with an L1 substrate-template duplex produces 3'-5' bonds exclusively. These results demonstrate how local geometry inherent to the substrate-template duplexes controls the regioselectivity of ribozyme-catalyzed RNA ligation reactions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21857665 D.M.Shechner, and D.P.Bartel (2011).
The structural basis of RNA-catalyzed RNA polymerization.
  Nat Struct Mol Biol, 18, 1036-1042.
PDB codes: 3r1h 3r1l
20554048 A.R.Ferré-D'Amaré (2010).
Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.
  Methods, 52, 159-167.  
20947767 J.N.Pitt, and A.R.Ferré-D'Amaré (2010).
Rapid construction of empirical RNA fitness landscapes.
  Science, 330, 376-379.  
20693400 J.N.Pitt, I.Rajapakse, and A.R.Ferré-D'Amaré (2010).
SEWAL: an open-source platform for next-generation sequence analysis and visualization.
  Nucleic Acids Res, 38, 7908-7915.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.