7U87

Product of 13mer primer with activated G monomer diastereomer 1

  • Classification: RNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2022-03-08 Released: 2023-03-15 
  • Deposition Author(s): Fang, Z., Szostak, J.W.
  • Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.188 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.

Fang, Z.Pazienza, L.T.Zhang, J.Tam, C.P.Szostak, J.W.

(2024) J Am Chem Soc 

  • DOI: https://doi.org/10.1021/jacs.4c00323
  • Primary Citation of Related Structures:  
    7U87, 7U88, 7U89, 7U8A, 8VAW, 8VAX

  • PubMed Abstract: 

    Nonenzymatic template-directed RNA copying requires catalysis by divalent metal ions. The primer extension reaction involves the attack of the primer 3'-hydroxyl on the adjacent phosphate of a 5'-5'-imidazolium-bridged dinucleotide substrate. However, the nature of the interaction of the catalytic metal ion with the reaction center remains unclear. To explore the coordination of the catalytic metal ion with the imidazolium-bridged dinucleotide substrate, we examined catalysis by oxophilic and thiophilic metal ions with both diastereomers of phosphorothioate-modified substrates. We show that Mg 2+ and Cd 2+ exhibit opposite preferences for the two phosphorothioate substrate diastereomers, indicating a stereospecific interaction of the divalent cation with one of the nonbridging phosphorus substituents. High-resolution X-ray crystal structures of the products of primer extension with phosphorothioate substrates reveal the absolute stereochemistry of this interaction and indicate that catalysis by Mg 2+ involves inner-sphere coordination with the nonbridging phosphate oxygen in the pro- S P position, while thiophilic cadmium ions interact with sulfur in the same position, as in one of the two phosphorothioate substrates. These results collectively suggest that during nonenzymatic RNA primer extension with a 5'-5'-imidazolium-bridged dinucleotide substrate the interaction of the catalytic Mg 2+ ion with the pro- S P oxygen of the reactive phosphate plays a crucial role in the metal-catalyzed S N 2(P) reaction.


  • Organizational Affiliation

    Department of Chemistry, Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(G46)P*(G46))-3')
A, B
15synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.188 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.741α = 90
b = 42.741β = 90
c = 83.28γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE 1607034
National Science Foundation (NSF, United States)United StatesCHE 2104708

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-04-17
    Changes: Database references