1G5D

NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation.

Hoehn, S.T.Turner, C.J.Stubbe, J.

(2001) Nucleic Acids Res. 29: 3413-3423

  • Primary Citation of Related Structures:  1G5E, 1GIZ, 1GJ0

  • PubMed Abstract: 
  • The antitumor antibiotic bleomycin causes two major lesions in the deoxyribose backbone of DNA: formation of 4'-keto abasic sites and formation of strand breaks with 3'-phosphoglycolate and 5'-phosphate ends. As a model for the 4'-keto abasic site, w ...

    The antitumor antibiotic bleomycin causes two major lesions in the deoxyribose backbone of DNA: formation of 4'-keto abasic sites and formation of strand breaks with 3'-phosphoglycolate and 5'-phosphate ends. As a model for the 4'-keto abasic site, we have characterized an abasic site (X) in d(CCAAAGXACTGGG).d(CCCAGTACTTTGG) by two-dimensional NMR spectroscopy. A total of 475 NOEs and 101 dihedral angles provided the restraints for molecular modeling. Four unusual NOEs were observed between each anomer of the abasic site and the neighboring bases. In addition, four coupling constants for adjacent protons of the deoxyribose of both the alpha and beta anomers of the abasic site were observed. The modeling suggests that for both anomers the abasic site is extrahelical, without significant distortion of the backbone opposite the lesion. The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic site in our structural model for each anomer is discussed in terms of repair of such lesions in vivo.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3'A13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'B13N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ORP
Query on ORP
A
SACCHARIDEC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance