2KH8

Solution Structure of cis-5R,6S-thymine glycol opposite complementary guanine in duplex DNA

Summary for 2KH8

• Entry DOI: 10.2210/pdb2kh8/pdb
• Related: 2KH7
• NMR Information: BMRB: 16226
• Descriptor: 5'-D(*GP*TP*GP*CP*GP*(CTG)P*GP*TP*TP*TP*GP*T)-3', 5'-D(*AP*CP*AP*AP*AP*CP*GP*CP*GP*CP*AP*C)-3' (2 entities in total)
• Functional Keywords: thymine glycol, dna
• Total number of polymer chains: 2
• Total formula weight: 7374.82

Authors

Brown, K.L. (deposition date: 2009-03-24, release date: 2009-12-01, Last modification date: 2024-05-22)

Primary citation

Brown, K.L.,Basu, A.K.,Stone, M.P.
The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA
Biochemistry, 48:9722-9733, 2009

PubMed Abstract: Oxidative damage to 5-methylcytosine in DNA, followed by deamination, yields thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, mispaired with deoxyguanosine. The structure of the 5R Tg.G mismatch pair has been refined using a combination of simulated annealing and isothermal molecular dynamics calculations restrained by NMR-derived distance restraints and torsion angle restraints in 5'-d(G(1)T(2)G(3)C(4)G(5)Tg(6)G(7)T(8)T(9)T(10)G(11)T(12))-3'.5'-d(A(13)C(14)A(15)A(16)A(17)C(18)G(19)C(20)G(21)C(22)A(23)C(24))-3'; Tg = 5R Tg. In this duplex the cis-5R,6S:trans-5R,6R equilibrium favors the cis-5R,6S epimer [Brown, K. L., Adams, T., Jasti, V. P., Basu, A. K., and Stone, M. P. (2008) J. Am. Chem. Soc. 130, 11701-11710]. The cis-5R,6S Tg lesion is in the wobble orientation such that Tg(6) O(2) is proximate to G(19) N1H and Tg(6) N3H is proximate to G(19) O(6). Both Tg(6) and the mismatched nucleotide G(19) remain stacked in the helix. The Tg(6) nucleotide shifts toward the major groove and stacks below the 5'-neighbor base G(5), while its complement G(19) stacks below the 5'-neighbor C(20). In the 3'-direction, stacking between Tg(6) and the G(7).C(18) base pair is disrupted. The solvent-accessible surface area of the Tg nucleotide increases as compared to the native Watson-Crick hydrogen-bonded T.A base pair. An increase in T(2) relaxation rates for the Tg(6) base protons is attributed to puckering of the Tg base, accompanied by increased disorder at the Tg.G mismatch pair. The axial vs equatorial conformation of the Tg(6) CH(3) group cannot be determined with certainty from the NMR data. The rMD trajectories suggest that in either the axial or equatorial conformations the cis-5R,6S Tg lesion does not form strong intrastrand hydrogen bonds with the imidazole N7 atom of the 3'-neighbor purine G(7). The wobble pairing and disorder of the Tg.G mismatch correlate with the reduced thermodynamic stability of the mismatch and likely modulate its recognition by DNA base excision repair systems.

PubMed: 19772348
DOI: 10.1021/bi900695e

Experimental method

SOLUTION NMR