6UFK

Pistol ribozyme product crystal soaked in Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crucial Roles of Two Hydrated Mg2+Ions in Reaction Catalysis of the Pistol Ribozyme.

Teplova, M.Falschlunger, C.Krasheninina, O.Egger, M.Ren, A.Patel, D.J.Micura, R.

(2019) Angew.Chem.Int.Ed.Engl. --: --

  • DOI: 10.1002/anie.201912522
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pistol ribozymes constitute a new class of small self-cleaving RNAs. We have solved crystal structures that provide three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, ...

    Pistol ribozymes constitute a new class of small self-cleaving RNAs. We have solved crystal structures that provide three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, a vanadate mimic of the transition state, and the product. The resulting architectonic framework dictates the proposed underlying chemical mechanism, which is corroborated by functional assays that involve atomic mutagenesis of the ribozyme. Importantly, a hydrated Mg2+ ion remains innersphere-coordinated to N7-G33 in all three states. This is consistent with its likely role as acid in general acid base catalysis (δ and ß catalysis), supported further by the observation of a more than 1000-fold rate reduction if its positioning is impaired by deletion of the N7 site. Strikingly, the new structures shed light on a second hydrated Mg2+ ion that approaches the scissile phosphate from its binding site in the pre-cleavage state to reach out for water-mediated H-bonding in the cyclophosphate product. Because this second hydrated Mg2+ ion is also close to the 6-oxygen atom of G40 (general base, γ catalysis), its potential impact on activation of G40 has been experimentally evaluated, however, the major role of the second Mg2+ ion appears to be the stabilization of product conformation. Together, our study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage with unprecedented precision.


    Organizational Affiliation

    University of Innsbruck, Institute of Organic Chemistry and Center for Molecular Biosciences, AUSTRIA.,Zhejiang University, Life Sciences Institute, CHINA.,Leopold-Franzens University, Institute of Organic Chemistry, Innrain 80-82, 6020, Innsbruck, AUSTRIA.,Memorial Sloan Kettering Cancer Center, Structural Biology Program, UNITED STATES.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (50-MER)A,C51synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3')B,D10synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*CP*CP*AP*G)-3')E,F5synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C, D, E, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
23G
Query on 23G
B, D
RNA OH 3 prime terminusC10 H13 N5 O10 P2G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 90.346α = 90.00
b = 90.346β = 90.00
c = 121.732γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United States--

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Source and taxonomy
  • Version 1.2: 2020-01-22
    Type: Database references