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| - | [[Image:2hsr.gif|left|200px]] | |
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| - | {{Structure
| + | ==13mer duplex DNA containing an abasic site with beta anomer== |
| - | |PDB= 2hsr |SIZE=350|CAPTION= <scene name='initialview01'>2hsr</scene>
| + | <StructureSection load='2hsr' size='340' side='right'caption='[[2hsr]]' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=B1P:2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSE'>B1P</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=[[2hsk|2HSK]], [[2hsl|2HSL]], [[2hou|2HOU]], [[2hpk|2HPK]], [[2hss|2HSS]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsr OCA], [http://www.ebi.ac.uk/pdbsum/2hsr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hsr RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''13mer duplex DNA containing an abasic site with beta anomer'''
| + | [[Category: Synthetic construct]] |
| - | | + | [[Category: Case DA]] |
| - | | + | [[Category: Chen J]] |
| - | ==Overview==
| + | [[Category: Dupradeau FY]] |
| - | 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.
| + | [[Category: Stubbe J]] |
| - | | + | [[Category: Turner CJ]] |
| - | ==About this Structure==
| + | |
| - | 2HSR is a [[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=2HSR OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17323932 17323932]
| + | |
| - | [[Category: Protein complex]]
| + | |
| - | [[Category: Case, D A.]]
| + | |
| - | [[Category: Chen, J.]] | + | |
| - | [[Category: Dupradeau, F Y.]] | + | |
| - | [[Category: Stubbe, J.]] | + | |
| - | [[Category: Turner, C J.]] | + | |
| - | [[Category: abasic site]] | + | |
| - | [[Category: ape1]] | + | |
| - | [[Category: base excision repair]] | + | |
| - | [[Category: dna damage]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:34:57 2008''
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