2KAR

HNE-dG adduct mismatched with dA in acidic solution


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conformational interconversion of the trans-4-hydroxynonenal-derived (6S,8R,11S) 1,N(2)-deoxyguanosine adduct when mismatched with deoxyadenosine in DNA

Huang, H.Wang, H.Lloyd, R.S.Rizzo, C.J.Stone, M.P.

(2009) Chem Res Toxicol 22: 187-200

  • DOI: 10.1021/tx800320m
  • Primary Citation of Related Structures:  
    2KAR, 2KAS

  • PubMed Abstract: 
  • The (6S,8R,11S) 1,N(2)-HNE-dGuo adduct of trans-4-hydroxynonenal (HNE) was incorporated into the duplex 5'-d(GCTAGCXAGTCC)-3'.5'-d(GGACTAGCTAGC)-3' [X = (6S,8R,11S) HNE-dG], in which the lesion was mismatched opposite dAdo. The (6S,8R,11S) adduct maintained the ring-closed 1,N(2)-HNE-dG structure ...

    The (6S,8R,11S) 1,N(2)-HNE-dGuo adduct of trans-4-hydroxynonenal (HNE) was incorporated into the duplex 5'-d(GCTAGCXAGTCC)-3'.5'-d(GGACTAGCTAGC)-3' [X = (6S,8R,11S) HNE-dG], in which the lesion was mismatched opposite dAdo. The (6S,8R,11S) adduct maintained the ring-closed 1,N(2)-HNE-dG structure. This was in contrast to when this adduct was correctly paired with dCyd, conditions under which it underwent ring opening and rearrangement to diastereomeric minor groove cyclic hemiacetals [ Huang , H. , Wang , H. , Qi , N. , Lloyd , R. S. , Harris , T. M. , Rizzo , C. J. , and Stone , M. P. ( 2008 ) J. Am. Chem. Soc. 130 , 10898 - 10906 ]. The (6S,8R,11S) adduct exhibited a syn/anti conformational equilibrium about the glycosyl bond. The syn conformation was predominant in acidic solution. Structural analysis of the syn conformation revealed that X(7) formed a distorted base pair with the complementary protonated A(18). The HNE moiety was located in the major groove. Structural perturbations were observed at the neighbor C(6).G(19) and A(8).T(17) base pairs. At basic pH, the anti conformation of X(7) was the major species. The 1,N(2)-HNE-dG intercalated and displaced the complementary A(18) in the 5'-direction, resulting in a bulge at the X(7).A(18) base pair. The HNE aliphatic chain was oriented toward the minor groove. The Watson-Crick hydrogen bonding of the neighboring A(8).T(17) base pair was also disrupted.


    Organizational Affiliation

    Department of Chemistry, Center in Molecular Toxicology, Center for Structural Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*DGP*DCP*DTP*DAP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DC)-3'A12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*DGP*DGP*DAP*DCP*DTP*DAP*DGP*DCP*DTP*DAP*DGP*DC)-3'B12N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HND
Query on HND

Download Ideal Coordinates CCD File 
C [auth A](4S)-nonane-1,4-diol
C9 H20 O2
BBKPDHOKNRMWQN-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations