3I2R

Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.

Spitale, R.C.Volpini, R.Mungillo, M.V.Krucinska, J.Cristalli, G.Wedekind, J.E.

(2009) Biochemistry 48: 7777-7779

  • DOI: 10.1021/bi9011622
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 thes ...

    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.


    Organizational Affiliation

    Department of Biochemistry & Biophysics, 601 Elmwood Avenue, Box 712, Rochester New York 14642, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'A14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (30-MER)B30N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'C19N/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

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Download CCD File 
B, C
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
S9L
Query on S9L
B
NON-POLYMERC6 H15 O7 P

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1DP
Query on 1DP
B
RNA LINKINGC11 H15 N4 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.650α = 90.00
b = 93.650β = 90.00
c = 132.240γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSphasing
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance