1M5V

Transition State Stabilization by a Catalytic RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.221 
  • R-Value Observed: 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:  
    1M5P, 1M5O, 1M5V

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN AG [auth C], H [auth F]100Homo sapiensMutation(s): 2 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA INHIBITOR SUBSTRATEA, D12N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA INHIBITOR SUBSTRATEB [auth M], E [auth P]9N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Find similar nucleic acids by:  (by identity cutoff)  |  Structure
      Entity ID: 3
      MoleculeChainsLengthOrganismImage
      RNA HAIRPIN RIBOZYMEC [auth B], F [auth E]92N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MPD
      Query on MPD

      Download Ideal Coordinates CCD File 
      QA [auth C], RA [auth F](4S)-2-METHYL-2,4-PENTANEDIOL
      C6 H14 O2
      SVTBMSDMJJWYQN-YFKPBYRVSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      AA [auth E] , BA [auth E] , CA [auth E] , DA [auth E] , EA [auth E] , FA [auth E] , GA [auth E] , HA [auth E] , 
      AA [auth E],  BA [auth E],  CA [auth E],  DA [auth E],  EA [auth E],  FA [auth E],  GA [auth E],  HA [auth E],  I [auth B],  IA [auth E],  J [auth B],  JA [auth E],  K [auth B],  KA [auth E],  L [auth B],  LA [auth E],  M [auth B],  MA [auth E],  N [auth B],  NA [auth E],  O [auth B],  OA [auth E],  P [auth B],  PA [auth C],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth D],  V [auth D],  W [auth P],  X [auth E],  Y [auth E],  Z [auth E]
      CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.40 Å
      • R-Value Free: 0.265 
      • R-Value Work: 0.221 
      • R-Value Observed: 0.221 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 258.648α = 90
      b = 44.258β = 107.69
      c = 102.174γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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