5EAQ

Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.201 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.

Mir, A.Golden, B.L.

(2016) Biochemistry 55: 633-636

  • DOI: 10.1021/acs.biochem.5b01139
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the ...

    The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.


    Related Citations: 
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (48-MER)A48synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3')B20synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CVC
Query on CVC
B
RNA linkingC9 H14 N3 O10 P V

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.201 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.247 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.251α = 90.00
b = 87.419β = 90.00
c = 105.539γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-10-16 
  • Released Date: 2016-02-24 
  • Deposition Author(s): Mir, A., Golden, B.L.

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release