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New page: left|200px<br /><applet load="1ii1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ii1" /> '''Structural Basis for Poor Uracil Excision fr...
 
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[[Image:1ii1.gif|left|200px]]<br /><applet load="1ii1" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ii1" />
'''Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study'''<br />


==Overview==
==Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study==
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. &amp; Varshney, U. (1997), Nucleic Acids Res. 25, 2336-2343.].
<StructureSection load='1ii1' size='340' side='right'caption='[[1ii1]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ii1]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1II1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1II1 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ii1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ii1 OCA], [https://pdbe.org/1ii1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ii1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ii1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ii1 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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. &amp; Varshney, U. (1997) Nucleic Acids Res. 25, 2336-2343.].


==About this Structure==
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<ref>PMID:11952790</ref>
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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1II1 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1ii1" style="background-color:#fffaf0;"></div>
[[Category: Chary, K.V.]]
== References ==
[[Category: Ghosh, M.]]
<references/>
[[Category: Rumpal, N.]]
__TOC__
[[Category: Varshney, U.]]
</StructureSection>
[[Category: double helix]]
[[Category: Large Structures]]
[[Category: hairpin dna]]
[[Category: Chary KV]]
[[Category: hairpin loop]]
[[Category: Ghosh M]]
[[Category: udg-uracil interaction]]
[[Category: Rumpal N]]
[[Category: uracil]]
[[Category: Varshney U]]
 
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