185D

SEQUENCE SPECIFICITY OF QUINOXALINE ANTIBIOTICS. 1. SOLUTION STRUCTURE OF A 1:1 COMPLEX BETWEEN TRIOSTIN A AND [D(GACGTC)]2 AND COMPARISON WITH THE SOLUTION STRUCTURE OF THE [N-MECYS3, N-MECYS7]TANDEM-[D(GATATC)]2 COMPLEX

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 5 

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This is version 1.5 of the entry. See complete history. 


Literature

Sequence Specificity of Quinoxaline Antibiotics. 1. Solution Structure of a 1:1 Complex between Triostin a and [D(Gacgtc)]2 and Comparison with the Solution Structure of the [N-Mecys3,N-Mecys7]Tandem-[D(Gatatc)]2 Complex.

Addess, K.J., Feigon, J.

(1994) Biochemistry 33: 12386

  • DOI: https://doi.org/10.1021/bi00207a005
  • Primary Citation of Related Structures:  
    185D

  • PubMed Abstract: 

    • Triostin A, a naturally occurring quinoxaline antibiotic that contains N-methyl groups on the valine and cysteine residues, binds sequence specifically to DNA at NCGN sites. [N-MeCys3,N-MeCys7]-TANDEM (CysMeTANDEM), a synthetic quinoxaline antibiotic, differs in its chemical structure from triostin A only at the valine residues, which contain no N-methyl substituents ...

    Triostin A, a naturally occurring quinoxaline antibiotic that contains N-methyl groups on the valine and cysteine residues, binds sequence specifically to DNA at NCGN sites. [N-MeCys3,N-MeCys7]-TANDEM (CysMeTANDEM), a synthetic quinoxaline antibiotic, differs in its chemical structure from triostin A only at the valine residues, which contain no N-methyl substituents. CysMeTANDEM has a sequence specificity different from triostin A, binding specifically to DNA at NTAN sites. To understand the factors that determine the sequence specificity of these quinoxaline antibiotics, the solution structure of a 1:1 complex of triostin A with the DNA hexamer [d(GACGTC)]2 has been determined using NMR-derived distance and dihedral angle restraints. The solution structure of the triostin A-[d(GACGTC)]2 complex is compared directly to the solution structure of a 1:1 complex of CysMeTANDEM with [d(GATATC)]2 and is also compared to the crystal structure of 2:1 complex of triostin A with [d(CGTACG)]2. Triostin A binds to [d(GACGTC)]2 as a bis-intercalator around the CpG step, and the peptide ring of the drug binds in the minor groove of the DNA. The central C.G base pairs of the complex are underwound with an average helical twist angle of approximately -9.0 degrees and buckle inward by about 25 degrees. There are intermolecular hydrogen bonds between each of the Ala NH and the GN3 protons of the CpG binding site. Similar structural features are observed in the solution structure of the CysMeTANDEM-[d(GATATC)]2 complex. However, in the structure of the triostin A-[d(GACGTC)]2 complex, two intermolecular hydrogen bonds between each of the Ala CO oxygens of the drug and the 2-amino protons of guanine are observed. These hydrogen bonds do not form in the CysMeTANDEM-DNA complex. Instead, CysMeTANDEM contains two intramolecular hydrogen bonds between the Ala CO atoms and the Val amide protons, making the Ala CO atoms unavailable to form two intermolecular hydrogen bonds. The role of these intermolecular hydrogen bonds in the CpG specificity of triostin A is discussed.

    Related Citations: 
    • Solution Structure of a Complex between [N-Mecys3,N-Mecys7]Tandem and [D(Gatatc)]2
      Addess, K.J., Sinsheimer, J.S., Feigon, J.
      (1993) Biochemistry 32: 2498
    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of California, Los Angeles 90024-1569.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRIOSTIN A8Streptomyces sp.Mutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*CP*GP*TP*C)-3')B [auth C],
C [auth D]		6N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUI
Query on QUI
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		2-CARBOXYQUINOXALINE
C9 H6 N2 O2
UPUZGXILYFKSGE-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MVA
Query on MVA
A
L-PEPTIDE LINKINGC6 H13 N O2VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000488
Query on PRD_000488
A
TRIOSTIN ACyclic depsipeptide / Anticancer Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 5 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2013-02-27
    Changes: Other
  • Version 1.5: 2017-11-01
    Changes: Advisory, Derived calculations, Other