1ZFT

The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage site

  • Classification: RNA

  • Deposited: 2005-04-20 Released: 2006-02-14 
  • Deposition Author(s): Wedekind, J.E.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer.

Salter, J.Krucinska, J.Alam, S.Grum-Tokars, V.Wedekind, J.E.

(2006) Biochemistry 45: 686-700

  • DOI: 10.1021/bi051887k
  • Primary Citation of Related Structures:  1ZFR, 1ZFV, 1ZFX, 2BCY, 2BCZ, 2OUE, 2FGP
  • Also Cited By: 2P7D, 2P7E, 2P7F

  • PubMed Abstract: 
  • The hairpin ribozyme requires functional group contributions from G8 to assist in phosphodiester bond cleavage. Previously, replacement of G8 by a series of nucleobase variants showed little effect on interdomain docking, but a 3-250-fold effect on c ...

    The hairpin ribozyme requires functional group contributions from G8 to assist in phosphodiester bond cleavage. Previously, replacement of G8 by a series of nucleobase variants showed little effect on interdomain docking, but a 3-250-fold effect on catalysis. To identify G8 features that contribute to catalysis within the hairpin ribozyme active site, structures for five base variants were determined by X-ray crystallography in a resolution range between 2.3 and 2.7 A. For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolution. The native structure revealed a scissile bond angle (tau) of 158 degrees, which is close to the requisite 180 degrees "in-line" geometry. Mutations G8(inosine), G8(diaminopurine), G8(aminopurine), G8(adenosine), and G8(uridine) folded properly, but exhibited nonideal scissile bond geometries (tau ranging from 118 degrees to 93 degrees) that paralleled their diminished solution activities. A superposition ensemble of all structures, including a previously described hairpin ribozyme-vanadate complex, indicated the scissile bond can adopt a variety of conformations resulting from perturbation of the chemical environment and provided a rationale for how the exocyclic amine of nucleobase 8 promotes productive, in-line geometry. Changes at position 8 also caused variations in the A-1 sugar pucker. In this regard, variants A8 and U8 appeared to represent nonproductive ground states in which their 2'-OH groups mimicked the pro-R, nonbridging oxygen of the vanadate transition-state complex. Finally, the results indicated that ordered water molecules bind near the 2'-hydroxyl of A-1, lending support to the hypothesis that solvent may play an important role in the reaction.


    Related Citations: 
    • Crystallization and x-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme
      Grum-Tokars, V.,Milovanovic, M.,Wedekind, J.E.
      (2003) Acta Crystallogr.,Sect.D 59: 142
    • Functional involvement of G8 in the hairpin ribozyme cleavage mechanism
      Pinard, R.,Hampel, K.J.,Heckman, J.E.,Lambert, D.,Chan, P.A.,Major, F.,Burke, J.M.
      (2001) Embo J. 20: 6434


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3'A13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3'B12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'C17N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'D19N/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, D
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
A
RNA LINKINGC11 H16 N5 O7 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.400α = 90.00
b = 93.400β = 90.00
c = 131.500γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
CrystalCleardata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-04-20 
  • Released Date: 2006-02-14 
  • Deposition Author(s): Wedekind, J.E.

Revision History 

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance