|
|
| (2 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
|
| |
|
| ==13mer duplex DNA containing an abasic site with beta anomer== | | ==13mer duplex DNA containing an abasic site with beta anomer== |
| <StructureSection load='2hsr' size='340' side='right'caption='[[2hsr]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | | <StructureSection load='2hsr' size='340' side='right'caption='[[2hsr]]' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[2hsr]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2HSR FirstGlance]. <br> | | <table><tr><td colspan='2'>[[2hsr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HSR FirstGlance]. <br> |
| </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</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">[[2hsk|2hsk]], [[2hsl|2hsl]], [[2hou|2hou]], [[2hpk|2hpk]], [[2hss|2hss]]</td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</scene></td></tr> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2hsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsr OCA], [http://pdbe.org/2hsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hsr RCSB], [http://www.ebi.ac.uk/pdbsum/2hsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsr ProSAT]</span></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=2hsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsr OCA], [https://pdbe.org/2hsr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hsr RCSB], [https://www.ebi.ac.uk/pdbsum/2hsr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsr ProSAT]</span></td></tr> |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
| |
| == Publication Abstract from PubMed ==
| |
| A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.
| |
|
| |
| Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites.,Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:17323932<ref>PMID:17323932</ref>
| |
|
| |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| |
| </div>
| |
| <div class="pdbe-citations 2hsr" style="background-color:#fffaf0;"></div>
| |
| == References ==
| |
| <references/>
| |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Case, D A]] | | [[Category: Synthetic construct]] |
| [[Category: Chen, J]] | | [[Category: Case DA]] |
| [[Category: Dupradeau, F Y]] | | [[Category: Chen J]] |
| [[Category: Stubbe, J]] | | [[Category: Dupradeau FY]] |
| [[Category: Turner, C J]] | | [[Category: Stubbe J]] |
| [[Category: Abasic site]] | | [[Category: Turner CJ]] |
| [[Category: Ape1]]
| |
| [[Category: Base excision repair]]
| |
| [[Category: Dna]]
| |
| [[Category: Dna damage]]
| |