1MXJ

NMR solution structure of benz[a]anthracene-dG in ras codon 12,2; GGCAGXTGGTG

Summary for 1MXJ

• Entry DOI: 10.2210/pdb1mxj/pdb
• Descriptor: 5'-D(*GP*GP*CP*AP*GP*GP*TP*GP*GP*TP*G)-3', 5'-D(*CP*AP*CP*CP*AP*CP*CP*TP*GP*CP*C)-3', 1S,2R,3S,4R-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL (3 entities in total)
• Functional Keywords: dna adduct, b-like dna, dna
• Total number of polymer chains: 2
• Total formula weight: 6989.70

Authors

Kim, H.-Y.H.,Wilkinson, A.S.,Harris, C.M.,Harris, T.M.,Stone, M.P. (deposition date: 2002-10-02, release date: 2003-03-11, Last modification date: 2024-05-22)

Primary citation

Kim, H.-Y.H.,Wilkinson, A.S.,Harris, C.M.,Harris, T.M.,Stone, M.P.
Minor Groove Orientation for the (1S,2R,3S,4R)-N2-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxy-benz[a]anthracenyl)]-2'-deoxyguanosyl Adduct in the N-ras Codon 12 sequence
Biochemistry, 42:2328-2338, 2003

PubMed Abstract: The conformation of the trans-anti-(1S,2R,3S,4R)-N(2)-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyguanosyl adduct in d(G(1)G(2)C(3)A(4)G(5)X(6)T(7)G(8)G(9)T(10)G(11)).d(C(12)A(13)C(14)C(15)A(16)C(17)C(18)T(19)G(20)C(21)C(22)), bearing codon 12 of the human N-ras protooncogene (underlined), was determined. This adduct had S stereochemistry at the benzylic carbon. Its occurrence in DNA is a consequence of trans opening by the deoxyguanosine amino group of (1R,2S,3S,4R)-1,2-epoxy-1,2,3,4-tetrahydrobenz[a]anthracenyl-3,4-diol. The resonance frequencies, relative to the unmodified DNA, of the X(6) H1' and H6 protons were shifted downfield, whereas those of the C(18) and T(19) H1', H2', H2' ', and H3' deoxyribose protons were shifted upfield. The imino and amino resonances exhibited the expected sequential connectivities, suggesting no interruption of Watson-Crick pairing. A total of 426 interproton distances, including nine uniquely assigned BA-DNA distances, were used in the restrained molecular dynamics calculations. The refined structure showed that the benz[a]anthracene moiety bound in the minor groove, in the 5'-direction from the modified site. This was similar to the (+)-trans-anti-benzo[a]pyrene-N(2)-dG adduct having S stereochemistry at the benzylic carbon [Cosman, M., De Los Santos, C., Fiala, R., Hingerty, B. E., Singh, S. B., Ibanez, V., Margulis, L. A., Live, D., Geacintov, N. E., Broyde, S., and Patel, D. J. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1914-1918]. It differed from the (-)-trans-anti-benzo[c]phenanthrene-N(2)-dG adduct having S stereochemistry at the benzylic carbon, which intercalated in the 5'-direction [Lin, C. H., Huang, X., Kolbanovskii, A., Hingerty, B. E., Amin, S., Broyde, S., Geacintov, N. E., and Patel, D. J. (2001) J. Mol. Biol. 306, 1059-1080]. The results provided insight into how PAH molecular topology modulates adduct structure in duplex DNA.

PubMed: 12600200
DOI: 10.1021/bi020462k

Experimental method

SOLUTION NMR