1M5V

Transition State Stabilization by a Catalytic RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Transition state stabilization by a catalytic RNA

Rupert, P.B.Massey, A.P.Sigurdsson, S.T.Ferre-D'Amare, A.R.

(2002) Science 298: 1421-1424

  • DOI: 10.1126/science.1076093
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of th ...

    The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of the 2.2 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor and product complexes reveals a rigid active site that makes more hydrogen bonds to the transition state than to the precursor or product. Because of the paucity of RNA functional groups capable of general acid-base or electrostatic catalysis, transition state stabilization is likely to be an important catalytic strategy for ribozymes.


    Related Citations: 
    • Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
      Rupert, P.B.,Ferre-D'Amare, A.R.
      (2001) Nature 410: 780


    Organizational Affiliation

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
C, F
100Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 1
MoleculeChainsLengthOrganism
RNA INHIBITOR SUBSTRATEA,D12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA INHIBITOR SUBSTRATEM,P9N/A
Entity ID: 3
MoleculeChainsLengthOrganism
RNA HAIRPIN RIBOZYMEB,E92N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, C, D, E, P
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
C, F
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A23
Query on A23
A, D
RNA LINKINGC10 H13 N5 O9 P2A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 258.648α = 90.00
b = 44.258β = 107.69
c = 102.174γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-12
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance