2BQ2

Solution Structure of the DNA Duplex ACGCGU-NA with a 2' Amido-Linked Nalidixic Acid Residue at the 3' Terminal Nucleotide


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST CALCULATED ENERGIES 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it.

Siegmund, K.Maheshwary, S.Narayanan, S.Connors, W.Riedrich, M.Printz, M.Richert, C.

(2005) Nucleic Acids Res. 33: 4838-4848

  • DOI: 10.1093/nar/gki795

  • PubMed Abstract: 
  • Quinolones are antibacterial drugs that are thought to bind preferentially to disturbed regions of DNA. They do not fall into the classical categories of intercalators, groove binders or electrostatic binders to the backbone. We solved the 3D structu ...

    Quinolones are antibacterial drugs that are thought to bind preferentially to disturbed regions of DNA. They do not fall into the classical categories of intercalators, groove binders or electrostatic binders to the backbone. We solved the 3D structure of the DNA duplex (ACGCGU-NA)2, where NA denotes a nalidixic acid residue covalently linked to the 2'-position of 2'-amino-2'-deoxyuridine, by NMR and restrained torsion angle molecular dynamics (MD). In the complex, the quinolones stack on G:C base pairs of the core tetramer and disrupt the terminal A:U base pair. The displaced dA residues can stack on the quinolones, while the uracil rings bind in the minor groove. The duplex-bridging interactions of the drugs and the contacts of the displaced nucleotides explain the high UV-melting temperature for d(ACGCGU-NA)2 of up to 53 degrees C. Further, non-covalently linked complexes between quinolones and DNA of the sequence ACGCGT can be generated via MD using constraints obtained for d(ACGCGU-NA)2. This is demonstrated for unconjugated nalidixic acid and its 6-fluoro derivative. The well-ordered and tightly packed structures thus obtained are compatible with a published model for the quinolone-DNA complex in the active site of gyrases.


    Organizational Affiliation

    Institute for Organic Chemistry, University of Karlsruhe, (TH) D-76131 Karlsruhe, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*CP*GP*CP*GP*2AU)-3'A,B6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NIX
Query on NIX

Download SDF File 
Download CCD File 
A, B
NALIDIXIC ACID
C12 H12 N2 O3
MHWLWQUZZRMNGJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2AU
Query on 2AU
A, B
RNA LINKINGC9 H14 N3 O8 PU
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST CALCULATED ENERGIES 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-03
    Type: Initial release
  • Version 1.1: 2013-05-01
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 2.0: 2018-05-09
    Type: Atomic model, Data collection, Database references