Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.97 kDa 
• Atom Count: 1340 
• Modelled Residue Count: 62 
• Deposited Residue Count: 62 
• Unique nucleic acid chains: 2
• Unique hybrid chains: 1

3CQS

A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases

• PDB DOI: 10.2210/pdb3CQS/pdb
• NDB: UR0138

• Classification: RNA
• Mutation(s): No 


• Deposited: 2008-04-03 Released: 2008-05-20 
• Deposition Author(s): Torelli, A.T., Spitale, R.C., Krucinska, J., Wedekind, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Literature

Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme

Torelli, A.T., Spitale, R.C., Krucinska, J., Wedekind, J.E.

(2008) Biochem Biophys Res Commun 371: 154-158

• PubMed: 18423397 
• DOI: 10.1016/j.bbrc.2008.04.036
• Primary Citation of Related Structures:  
  3CQS


• PubMed Abstract: 
  

Reaction-intermediate analogs have been used to understand how phosphoryl transfer enzymes promote catalysis. Herein we report the first structure of a small ribozyme crystallized with a 3'-OH, 2',5'-linkage in lieu of the normal phosphodiester substrate. The new structure shares features of the reaction coordinate exhibited in prior ribozyme structures including a vanadate complex that mimicked the oxyphosphorane transition state. As such, the structure exhibits reaction-intermediate traits that allow direct comparison of stabilizing interactions to the 3'-OH, 2',5'-linkage contributed by the RNA enzyme and its protein counterpart, ribonuclease. Clear similarities are observed between the respective structures including hydrogen bonds to the non-bridging oxygens of the scissile phosphate. Other commonalities include carefully poised water molecules that may alleviate charge build-up in the transition state and placement of a positive charge near the leaving group. The advantages of 2',5'-linkages to investigate phosphoryl-transfer reactions are discussed, and argue for their expanded use in structural studies.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue Box 712, Rochester, New York 14642, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
13-mer substrate strand with 3'-OH, 2',5'-phosphodiester covalently linking 5th and 6th nucleotides	A	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
29-mer ribozyme strand with S9L synthetic linker at 13th position	B	30	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
19-mer ribozyme strand	C	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	D [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-FGTKAUEHAT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.16	α = 90
b = 93.16	β = 90
c = 129.05	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-03 
• Released Date: 2008-05-20 
Deposition Author(s): Torelli, A.T., Spitale, R.C., Krucinska, J., Wedekind, J.E.

Revision History  

• Version 1.0: 2008-05-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance