3R1H

Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Ca2+ bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The structural basis of RNA-catalyzed RNA polymerization.

Shechner, D.M., Bartel, D.P.

(2011) Nat Struct Mol Biol 18: 1036-1042

  • DOI: 10.1038/nsmb.2107
  • Primary Citation of Related Structures:  
    3R1L, 3R1H

  • PubMed Abstract: 

    • Early life presumably required polymerase ribozymes capable of replicating RNA. Known polymerase ribozymes best approximating such replicases use as their catalytic engine an RNA-ligase ribozyme originally selected from random RNA sequences. Here we report 3 ...

    Early life presumably required polymerase ribozymes capable of replicating RNA. Known polymerase ribozymes best approximating such replicases use as their catalytic engine an RNA-ligase ribozyme originally selected from random RNA sequences. Here we report 3.15-Å crystal structures of this ligase trapped in catalytically viable preligation states, with the 3'-hydroxyl nucleophile positioned for in-line attack on the 5'-triphosphate. Guided by metal- and solvent-mediated interactions, the 5'-triphosphate hooks into the major groove of the adjoining RNA duplex in an unanticipated conformation. Two phosphates and the nucleophile jointly coordinate an active-site metal ion. Atomic mutagenesis experiments demonstrate that active-site nucleobase and hydroxyl groups also participate directly in catalysis, collectively playing a role that in proteinaceous polymerases is performed by a second metal ion. Thus artificial ribozymes can use complex catalytic strategies that differ markedly from those of analogous biological enzymes.

    Organizational Affiliation: 

    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A A, D98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
NIH Common Fund Data Resources
PHAROS:  P09012
GTEx:  ENSG00000077312
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*UP*CP*CP*AP*GP*UP*A)-3'B, E7N/A
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 3
    MoleculeChainsLengthOrganismImage
    Class I ligase ribozymeC, F130N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.15 Å
    • R-Value Free: 0.255 
    • R-Value Work: 0.212 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 58.69α = 99.847
    b = 70.011β = 99.735
    c = 71.858γ = 103.651
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    PHASERphasing
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2011-08-31
      Type: Initial release
    • Version 1.1: 2011-09-07
      Changes: Database references
    • Version 1.2: 2011-09-21
      Changes: Database references