1D17

DNA-NOGALAMYCIN INTERACTIONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

DNA-nogalamycin interactions.

Egli, M.Williams, L.D.Frederick, C.A.Rich, A.

(1991) Biochemistry 30: 1364-1372

  • DOI: 10.1021/bi00219a029
  • Primary Citation of Related Structures:  
    1D17

  • PubMed Abstract: 
  • The anthracycline antibiotic nogalamycin differs from the more common daunomycin-type anthracyclines by substitution on both ends of the intercalating chromophore, giving nogalamycin the approximate shape of a dumbbell. The chromophore of daunomycin is substituted on only one end ...

    The anthracycline antibiotic nogalamycin differs from the more common daunomycin-type anthracyclines by substitution on both ends of the intercalating chromophore, giving nogalamycin the approximate shape of a dumbbell. The chromophore of daunomycin is substituted on only one end. In nogalamycin, the positively charged amino sugar substituent of daunomycin is replaced by an uncharged nogalose sugar and a methyl ester group. The other end of nogalamycin, where daunomycin is unsubstituted, is fused to a bicyclo amino sugar with a positively charged dimethylamino group. Much larger DNA fluctuations are required for intercalative entry of nogalamycin than for entry of daunomycin. This report describes the X-ray crystal structure of the complex between nogalamycin and the self-complementary DNA hexamer d(me5CGTsAme5CG). The DNA contains cytosines methylated at the 5-positions and a phosphorothioate linkage at the TpA step. Nogalamycin intercalates at the terminal CpG steps and interacts with both strands in both grooves of the DNA. Large conformational adjustments in both nogalamycin and the DNA are necessary to form a stable, intercalative complex. The interactions of the bases with the nogalamycin substituents lead to sliding of bases relative to each other along the normal to Watson-Crick hydrogen bonds. The planarities of base pairs surrounding the intercalation site are distorted. The backbones of the two strands are distorted asymmetrically by nogalamycin with large deviations from standard B-DNA geometry. The complex between nogalamycin and DNA illustrates the conformational flexibility of DNA. The hydrogen-bonding interactions between nogalamycin and DNA do not suggest a sequence-specific binding of the drug, although additional secondary effects might lead to differences between various intercalation sites.


    Related Citations: 
    • Structure of Nogalamycin Bound to a DNA Hexamer
      Williams, L.D., Egli, M., Gao, Q., Bash, P., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Frederick, C.A.
      (1990) Proc Natl Acad Sci U S A 87: 2225

    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*(5CM)P*GP*TP*AP*(5CM)P*G)-3')A6N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NGM (Subject of Investigation/LOI)
    Query on NGM

    Download Ideal Coordinates CCD File 
    B [auth A]NOGALAMYCIN
    C39 H49 N O16
    KGTDRFCXGRULNK-JYOBTZKQSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Work: 0.206 
    • R-Value Observed: 0.206 
    • Space Group: P 61 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 26.3α = 90
    b = 26.3β = 90
    c = 100.01γ = 120
    Software Package:
    Software NamePurpose
    X-PLORrefinement

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1991-07-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2011-08-24
      Changes: Atomic model, Derived calculations