3I2R image
Deposition Date 2009-06-29
Release Date 2009-11-03
Last Version Date 2023-09-06
Entry Detail
PDB ID:
3I2R
Keywords:
RNA
Title:
Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9
Biological Source:
Source Organism:
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.80 Å
R-Value Free:
0.27
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 61 2 2
3I2R validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'
Chain IDs:A
Chain Length:14
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide/polyribonucleotide hybrid
Molecule:DNA/RNA (30-MER)
Chain IDs:B
Chain Length:30
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule:5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
Chain IDs:C
Chain Length:19
Number of Molecules:1
Biological Source:
Ligand Molecules
NCO
SO4
Primary Citation
Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.
Biochemistry 48 7777 7779 (2009)
PMID: 19634899 DOI: 10.1021/bi9011622

Abstact

The hairpin ribozyme cleaves a phosphodiester bond within a cognate substrate. Structural and biochemical data indicate the conserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalysis. To investigate these residues, we replaced the imino moiety of each base with N1-deazaadenosine. This single-atom change resulted in an 8-fold loss in k(obs) for A9 and displacement of the base from the active site; no effects were observed for A10. We propose that the imino moiety of A9 promotes a key water-mediated contact that favors transition-state formation, which suggests an enhanced chemical repertoire for RNA.

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Protein

Chemical

Disease

Primary Citation of related structures
3I2P
3I2Q
3I2S
3I2U