4G6P

Minimal Hairpin Ribozyme in the Precatalytic State with A38P Variation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.641 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis.

Liberman, J.A.Guo, M.Jenkins, J.L.Krucinska, J.Chen, Y.Carey, P.R.Wedekind, J.E.

(2012) J.Am.Chem.Soc. 134: 16933-16936

  • DOI: 10.1021/ja3070528
  • Primary Citation of Related Structures:  

  • PubMed 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 ri ...

    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.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Loop A Substrate strandA13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
Loop A and Loop B Ribozyme strandB30N/A
Entity ID: 3
MoleculeChainsLengthOrganism
Loop B of the Ribozyme StrandC19N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NCO
Query on NCO

Download SDF File 
Download CCD File 
B, C
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
A
RNA LINKINGC11 H16 N5 O7 PA
P5P
Query on P5P
C
RNA LINKINGC10 H13 N4 O7 PA
S9L
Query on S9L
B
NON-POLYMERC6 H15 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.641 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.185 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.664α = 90.00
b = 93.664β = 90.00
c = 134.270γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references