1HZ0

NMR STRUCTURE OF THE 2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE (PHIP) C8-DEOXYGUANOSINE ADDUCT IN DUPLEX DNA

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2001-01-23 Released: 2001-08-08 
  • Deposition Author(s): Brown, K., Cosman, M.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 48 
  • Conformers Submitted: 6 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Solution structure of the 2-amino-1- methyl-6-phenylimidazo[4,5-b]pyridine C8-deoxyguanosine adduct in duplex DNA.

Brown, K., Hingerty, B.E., Guenther, E.A., Krishnan, V.V., Broyde, S., Turteltaub, K.W., Cosman, M.

(2001) Proc Natl Acad Sci U S A 98: 8507-8512

  • DOI: 10.1073/pnas.151251898
  • Primary Citation of Related Structures:  
    1HZ0

  • PubMed Abstract: 

    • The carcinogenic heterocyclic amine (HA) 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is formed during the cooking of various meats. To enable structure/activity studies aimed at understanding how DNA damaged by a member of the HA class of compounds can ultimately lead to cancer, we have determined the first solution structure of an 11-mer duplex containing the C8-dG adduct formed by reaction with N-acetoxy-PhIP ...

    The carcinogenic heterocyclic amine (HA) 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is formed during the cooking of various meats. To enable structure/activity studies aimed at understanding how DNA damaged by a member of the HA class of compounds can ultimately lead to cancer, we have determined the first solution structure of an 11-mer duplex containing the C8-dG adduct formed by reaction with N-acetoxy-PhIP. A slow conformational exchange is observed in which the PhIP ligand either intercalates into the DNA helix by denaturing and displacing the modified base pair (main form) or is located outside the helix in a minimally perturbed B-DNA duplex (minor form). In the main base-displaced intercalation structure, the minor groove is widened, and the major groove is compressed at the lesion site because of the location of the bulky PhIP-N-methyl and phenyl ring in the minor groove; this distortion causes significant bending of the helix. The PhIP phenyl ring interacts with the phosphodiester-sugar ring backbone of the complementary strand and its fast rotation with respect to the intercalated imidazopyridine ring causes substantial distortions at this site, such as unwinding and bulging-out of the strand. The glycosidic torsion angle of the [PhIP]dG residue is syn, and the displaced guanine base is directed toward the 3' end of the modified strand. This study contributes, to our knowledge, the first structural information on the biologically relevant HA class to a growing body of knowledge about how conformational similarities and differences for a variety of types of lesions can influence protein interactions and ultimately biological outcome.

    Organizational Affiliation: 

    Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3')A 11N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3')B 11N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIQ
Query on PIQ
Download Ideal Coordinates CCD File 
C [auth A]2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE
C13 H12 N4
UQVKZNNCIHJZLS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 48 
  • Conformers Submitted: 6 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 1HZ0 Olderado

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2001-01-23 
  • Released Date: 2001-08-08 
    • Deposition Author(s): Brown, K., Cosman, M.

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations