2hsr: Difference between revisions

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New page: left|200px<br /><applet load="2hsr" size="350" color="white" frame="true" align="right" spinBox="true" caption="2hsr" /> '''13mer duplex DNA containing an abasic site w...
 
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[[Image:2hsr.gif|left|200px]]<br /><applet load="2hsr" size="350" color="white" frame="true" align="right" spinBox="true"
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'''13mer duplex DNA containing an abasic site with beta anomer'''<br />


==Overview==
==13mer duplex DNA containing an abasic site with beta anomer==
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.
<StructureSection load='2hsr' size='340' side='right'caption='[[2hsr]]' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
2HSR 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=2HSR OCA].  
</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='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>
==Reference==
<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>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17323932 17323932]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Case, D.A.]]
</StructureSection>
[[Category: Chen, J.]]
[[Category: Large Structures]]
[[Category: Dupradeau, F.Y.]]
[[Category: Synthetic construct]]
[[Category: Stubbe, J.]]
[[Category: Case DA]]
[[Category: Turner, C.J.]]
[[Category: Chen J]]
[[Category: abasic site]]
[[Category: Dupradeau FY]]
[[Category: ape1]]
[[Category: Stubbe J]]
[[Category: base excision repair]]
[[Category: Turner CJ]]
[[Category: dna damage]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:06:45 2008''

Latest revision as of 09:41, 1 May 2024

13mer duplex DNA containing an abasic site with beta anomer13mer duplex DNA containing an abasic site with beta anomer

Structural highlights

2hsr is a 2 chain structure with sequence from Synthetic construct. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT
Drag the structure with the mouse to rotate

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