3R1L

Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Mg2+ bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 ...

    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 AA, 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
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
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download CCD File 
    C, F
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.13 Å
    • R-Value Free: 0.240 
    • R-Value Work: 0.197 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 59.19α = 99.86
    b = 70.237β = 99.34
    c = 71.214γ = 103.81
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data collection
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • 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
    • Version 1.3: 2017-11-08
      Changes: Advisory, Refinement description