|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Structural Basis for Poor Excision from Hairpin DNA: NMR Study== | | ==Structural Basis for Poor Excision from Hairpin DNA: NMR Study== |
| - | <StructureSection load='1idx' size='340' side='right' caption='[[1idx]], [[NMR_Ensembles_of_Models | 6 NMR models]]' scene=''> | + | <StructureSection load='1idx' size='340' side='right'caption='[[1idx]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1idx]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IDX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1idx]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IDX FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene></td></tr> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ii1|1ii1]], [[1qe7|1qe7]], [[1dgo|1dgo]]</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=1idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1idx OCA], [https://pdbe.org/1idx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1idx RCSB], [https://www.ebi.ac.uk/pdbsum/1idx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1idx ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1idx OCA], [http://pdbe.org/1idx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1idx RCSB], [http://www.ebi.ac.uk/pdbsum/1idx PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| Line 20: |
Line 20: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Chary, K V]] | + | [[Category: Large Structures]] |
| - | [[Category: Ghosh, M]] | + | [[Category: Chary KV]] |
| - | [[Category: Rumpal, N]] | + | [[Category: Ghosh M]] |
| - | [[Category: Varshney, U]] | + | [[Category: Rumpal N]] |
| - | [[Category: Dna]]
| + | [[Category: Varshney U]] |
| - | [[Category: Double helix]]
| + | |
| - | [[Category: Hairpin dna]]
| + | |
| - | [[Category: Hairpin loop]]
| + | |
| - | [[Category: Udg-uracil interaction]]
| + | |
| - | [[Category: Uracil]]
| + | |
| Structural highlights
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. & Varshney, U. (1997) Nucleic Acids Res. 25, 2336-2343.].
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ghosh M, Rumpal N, Varshney U, Chary KV. Structural basis for poor uracil excision from hairpin DNA. An NMR study. Eur J Biochem. 2002 Apr;269(7):1886-94. PMID:11952790
|
