4G6P: Minimal Hairpin Ribozyme In The Precatalytic State With A38p Variation

Citation:
Abstract
One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pK(a) values for the Ade38 N1 imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pK(a) value of 6.27 +/- 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pK(a), we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pK(a) values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pK(a) > 0.8 log unit relative to the precatalytic state. The agreement of the microscopic and macroscopic pK(a) values and the accompanying structural analysis supports a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity.
PDB ID: 4G6PDownload
MMDB ID: 102039
PDB Deposition Date: 2012/7/19
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.64  Å
Source Organism:
Biological Unit for 4G6P: trimeric; determined by author and by software (PISA)
Molecular Components in 4G6P
Label Count Molecule
Nucleotides(3 molecules)
1
Loop a Substrate Strand
Molecule annotation
1
Loop a and Loop B Ribozyme Strand
Molecule annotation
1
Loop B of the Ribozyme Strand
Molecule annotation
Chemicals (3 molecules)
1
1
2
2
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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