1M5O

Transition State Stabilization by a Catalytic RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

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:  
    1M5O, 1M5P, 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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN AE [auth C], F100Homo 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
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA SUBSTRATEA, C [auth D]21N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA HAIRPIN RIBOZYMEB, D [auth E]92N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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] , G [auth A] , GA [auth E] , 
AA [auth E],  BA [auth E],  CA [auth E],  DA [auth E],  EA [auth E],  FA [auth E],  G [auth A],  GA [auth E],  H [auth A],  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 C],  M [auth B],  MA [auth C],  N [auth B],  NA [auth C],  O [auth B],  OA [auth C],  P [auth B],  PA [auth F],  Q [auth B],  QA [auth F],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth D],  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: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 259.38α = 90
b = 44.22β = 106.3
c = 102.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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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