3ZD5

THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis.

Martick, M.Scott, W.G.

(2006) Cell 126: 309

  • DOI: 10.1016/j.cell.2006.06.036
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Minimal hammerhead ribozymes have been characterized extensively by static and time-resolved crystallography as well as numerous biochemical analyses, leading to mutually contradictory mechanistic explanations for catalysis. We present the 2.2 A reso ...

    Minimal hammerhead ribozymes have been characterized extensively by static and time-resolved crystallography as well as numerous biochemical analyses, leading to mutually contradictory mechanistic explanations for catalysis. We present the 2.2 A resolution crystal structure of a full-length Schistosoma mansoni hammerhead ribozyme that permits us to explain the structural basis for its 1000-fold catalytic enhancement. The full-length hammerhead structure reveals how tertiary interactions occurring remotely from the active site prime this ribozyme for catalysis. G-12 and G-8 are positioned consistent with their previously suggested roles in acid-base catalysis, the nucleophile is aligned with a scissile phosphate positioned proximal to the A-9 phosphate, and previously unexplained roles of other conserved nucleotides become apparent within the context of a distinctly new fold that nonetheless accommodates the previous structural studies. These interactions permit us to explain the previously irreconcilable sets of experimental results in a unified, consistent, and unambiguous manner.


    Organizational Affiliation

    Department of Molecular, Cellular and Developmental Biology, Robert L. Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
HAMMERHEAD RIBOZYME, ENZYME STRANDA43synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
HAMMERHEAD RIBOZYME, SUBSTRATE STRANDB20synthetic construct
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
GDP
Query on GDP
A
RNA LINKINGC10 H15 N5 O11 P2G
5BU
Query on 5BU
B
RNA LINKINGC9 H12 Br N2 O9 PU
OMC
Query on OMC
B
RNA LINKINGC10 H16 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 49.886α = 90.00
b = 69.210β = 111.83
c = 60.076γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
CNSphasing
ADSCdata reduction
MOSFLMdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-11-24 
  • Released Date: 2012-12-12 
  • Deposition Author(s): Martick, M., Scott, W.G.
  • This entry supersedes: 2GOZ

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Other