1YY0

Crystal structure of an RNA duplex containing a 2'-amine substitution and a 2'-amide product produced by in-crystal acylation at a C-A mismatch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures, reactivity and inferred acylation transition States for 2'-amine substituted RNA.

Gherghe, C.M.Krahn, J.M.Weeks, K.M.

(2005) J Am Chem Soc 127: 13622-13628

  • DOI: 10.1021/ja053647y
  • Primary Citation of Related Structures:  
    1YRM, 1YY0, 1YZD, 1Z79, 1Z7F

  • PubMed Abstract: 
  • Ribose 2'-amine substitutions are broadly useful as structural probes in nucleic acids. In addition, structure-selective chemical reaction at 2'-amine groups is a robust technology for interrogating local nucleotide flexibility and conformational changes in RNA and DNA ...

    Ribose 2'-amine substitutions are broadly useful as structural probes in nucleic acids. In addition, structure-selective chemical reaction at 2'-amine groups is a robust technology for interrogating local nucleotide flexibility and conformational changes in RNA and DNA. We analyzed crystal structures for several RNA duplexes containing 2'-amino cytidine (C(N)) residues that form either C(N)-G base pairs or C(N)-A mismatches. The 2'-amine substitution is readily accommodated in an A-form RNA helix and thus differs from the C2'-endo conformation observed for free nucleosides. The 2'-amide product structure was visualized directly by acylating a C(N)-A mismatch in intact crystals and is also compatible with A-form geometry. To visualize conformations able to facilitate formation of the amide-forming transition state, in which the amine nucleophile carries a positive partial charge, we analyzed crystals of the C(N)-A duplex at pH 5, where the 2'-amine is protonated. The protonated amine moves to form a strong electrostatic interaction with the 3'-phosphodiester. Taken together with solution-phase experiments, 2'-amine acylation is likely facilitated by either of two transition states, both involving precise positioning of the adjacent 3'-phosphodiester group.


    Organizational Affiliation

    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'A, C 16N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*AP*GP*AP*(M5M)P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'B 16N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.6α = 90
b = 42.6β = 90
c = 121γ = 120
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model