1ii1
From Proteopedia
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'''Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study'''<br /> | '''Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Two-dimensional NMR and molecular dynamics simulations have been used to | + | 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== | ==About this Structure== | ||
| - | 1II1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1II1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1II1 OCA]. |
==Reference== | ==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11952790 11952790] | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11952790 11952790] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Chary, K | + | [[Category: Chary, K V.]] |
[[Category: Ghosh, M.]] | [[Category: Ghosh, M.]] | ||
[[Category: Rumpal, N.]] | [[Category: Rumpal, N.]] | ||
| Line 22: | Line 22: | ||
[[Category: uracil]] | [[Category: uracil]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:12:06 2008'' |
Revision as of 11:12, 21 February 2008
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Structural Basis for Poor Uracil 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
1II1 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
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