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1idx
From Proteopedia
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Structural Basis for Poor Excision from Hairpin DNA: NMR Study
Overview
Two-dimensional NMR and molecular dynamics simulations have been used to, determine the three-dimensional structures of two hairpin DNA structures:, d-CTAGAG GATCCUTTTGGATCCT (abbreviated as U1-hairpin) and, d-CTAGAGGATCCTTUTGGATCCT (abbreviated as U3-hairpin). The 1H resonances of, both of these hairpin structures have been assigned almost completely. NMR, restrained molecular dynamics and energy minimization procedures have been, used to describe the three-dimensional structures of these hairpins. This, study and concurrent NMR structural studies on two other d-CTAGAGGA, TCCTUTTGGATCCT (abbreviated as U2-hairpin) and d-CTAGAGGATCCTTTUGGATCCT, (abbreviated as U4-hairpin) have shed light upon various interactions, reported between Echerichia coli uracil DNA glycosylase (UDG) and, uracil-containing DNA. The backbone torsion angles, which partially, influence the local conformation of U12 and U14 in U1 and U3-hairpins, respectively, are probably locked in the trans conformation as in the case, of U13 in the U2-hairpin. Such a stretched-out backbone conformation in, the vicinity of U12 and U14 is thought to be the reason why the Km value, is poor for U1- and U3-hairpins as it is for the U2-hairpin. Furthermore, the bases U12 and U14 in both U1- and U3-hairpins adopt an anti, conformation, in contrast with the base conformation of U13 in the, U2-hairpin, which adopts a syn conformation. The clear discrepancy, observed in the U-base orientation with respect to the sugar moieties, could explain why the Vmax value is 10- to 20-fold higher for the U1- and, U3-hairpins compared with the U2-hairpin. Taken together, these, observations support our interpretation that the unfavourable backbone, results in a poor Km value, whereas the unfavourable nucleotide, conformation results in a poor Vmax value. These two parameters therefore, make the U1- and U3-hairpins better substrates for UDG compared with the, U2-hairpin, as reported earlier [Kumar, N. V. & Varshney, U. (1997), Nucleic Acids Res. 25, 2336-2343.].
About this Structure
1IDX is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structural basis for poor uracil excision from hairpin DNA. An NMR study., Ghosh M, Rumpal N, Varshney U, Chary KV, Eur J Biochem. 2002 Apr;269(7):1886-94. PMID:11952790
Page seeded by OCA on Sat Nov 24 21:51:13 2007
