5YTZ

Crystal structure of echinomycin-d(ACGTCGT)2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex

Wu, P.C.Tzeng, S.L.Chang, C.K.Kao, Y.F.Waring, M.J.Hou, M.H.

(2018) Nucleic Acids Res 46: 7396-7404

  • DOI: 10.1093/nar/gky345
  • Primary Citation of Related Structures:  
    5YTY, 5YTZ

  • PubMed Abstract: 
  • Small-molecule compounds that target mismatched base pairs in DNA offer a novel prospective for cancer diagnosis and therapy. The potent anticancer antibiotic echinomycin functions by intercalating into DNA at CpG sites. Surprisingly, we found that t ...

    Small-molecule compounds that target mismatched base pairs in DNA offer a novel prospective for cancer diagnosis and therapy. The potent anticancer antibiotic echinomycin functions by intercalating into DNA at CpG sites. Surprisingly, we found that the drug strongly prefers to bind to consecutive CpG steps separated by a single T:T mismatch. The preference appears to result from enhanced cooperativity associated with the binding of the second echinomycin molecule. Crystallographic studies reveal that this preference originates from the staggered quinoxaline rings of the two neighboring antibiotic molecules that surround the T:T mismatch forming continuous stacking interactions within the duplex. These and other associated changes in DNA conformation allow the formation of a minor groove pocket for tight binding of the second echinomycin molecule. We also show that echinomycin displays enhanced cytotoxicity against mismatch repair-deficient cell lines, raising the possibility of repurposing the drug for detection and treatment of mismatch repair-deficient cancers.


    Organizational Affiliation

    Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan.



Macromolecules

  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EchinomycinD, F8Streptomyces echinatusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*CP*GP*TP*CP*GP*(UD))-3')A, B7unidentified
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    QUI
    Query on QUI

    Download CCD File 
    D, F
    2-CARBOXYQUINOXALINE
    C9 H6 N2 O2
    UPUZGXILYFKSGE-UHFFFAOYSA-N
     Ligand Interaction
    MN
    Query on MN

    Download CCD File 
    A, B
    MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download CCD File 
    D
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    MVA
    Query on MVA
    D,FL-PEPTIDE LINKINGC6 H13 N O2VAL
    Biologically Interesting Molecules (External Reference) 1 Unique
    Entity ID: 2
    IDChainsNameType/Class2D Diagram3D Interactions
    PRD_000491
    Query on PRD_000491
    D, FEchinomycinCyclic depsipeptide /  Antibiotic

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    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.55 Å
    • R-Value Free: 0.235 
    • R-Value Work: 0.206 
    • R-Value Observed: 0.209 
    • Space Group: I 41 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 41.759α = 90
    b = 41.759β = 90
    c = 138.415γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data reduction
    HKL-2000data scaling
    Cootmodel building
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2018-05-23
      Type: Initial release
    • Version 1.1: 2018-05-30
      Changes: Data collection, Database references, Structure summary
    • Version 1.2: 2018-09-05
      Changes: Data collection, Database references