5DI4

Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mn2+ at low pH

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

  • Deposited: 2015-08-31 Released: 2015-10-07 
  • Deposition Author(s): Mir, A., Chen, J., Neau, D., Golden, B.L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.

Mir, A.Chen, J.Robinson, K.Lendy, E.Goodman, J.Neau, D.Golden, B.L.

(2015) Biochemistry 54: 6369-6381

  • DOI: 10.1021/acs.biochem.5b00824
  • Primary Citation of Related Structures:  
    5DH6, 5DH7, 5DH8, 5DI2, 5DI4, 5DQK

  • PubMed Abstract: 
  • The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer ...

    The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer. Metal ions have been implicated in the chemical mechanism, but no interactions between divalent metal ions and the cleavage site have been observed crystallographically. To better understand how this ribozyme functions, we have solved crystal structures of wild-type and G12A mutant ribozymes. We observe a pH-dependent conformational change centered around G12, consistent with this nucleotide becoming deprotonated. Crystallographic and kinetic analysis of the G12A mutant reveals a Zn(2+) specificity switch suggesting a direct interaction between a divalent metal ion and the purine at position 12. The metal ion specificity switch and the pH-rate profile of the G12A mutant suggest that the minor imino tautomer of A12 serves as the general base in the mutant ribozyme. We propose a model in which the hammerhead ribozyme rearranges prior to the cleavage reaction, positioning two divalent metal ions in the process. The first metal ion, positioned near G12, becomes directly coordinated to the O6 keto oxygen, to lower the pKa of the general base and organize the active site. The second metal ion, positioned near G10.1, bridges the N7 of G10.1 and the scissile phosphate and may participate directly in the cleavage reaction.


    Organizational Affiliation

    Department of Biochemistry, Purdue University , West Lafayette, Indiana 47907, United States.



Macromolecules
Find similar nucleic acids by: Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (48-MER)A48synthetic construct
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'B20synthetic construct
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.95 Å
    • R-Value Free: 0.233 
    • R-Value Work: 0.209 
    • R-Value Observed: 0.212 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 80.169α = 90
    b = 85.923β = 90
    c = 104.258γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM095923

    Revision History  (Full details and data files)

    • Version 1.0: 2015-10-07
      Type: Initial release
    • Version 1.1: 2015-11-04
      Changes: Database references
    • Version 1.2: 2017-09-27
      Changes: Author supporting evidence, Database references, Derived calculations
    • Version 1.3: 2019-12-25
      Changes: Author supporting evidence