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 1.3 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],
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
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],
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
  • Version 1.3: 2021-10-27
    Changes: Advisory, Database references, Derived calculations