2hsk

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2hsk" size="350" color="white" frame="true" align="right" spinBox="true" caption="2hsk" /> '''NMR Structure of 13mer Duplex DNA containing...)
Current revision (06:41, 1 May 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2hsk.gif|left|200px]]<br /><applet load="2hsk" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2hsk" />
 
-
'''NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)'''<br />
 
-
==Overview==
+
==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha 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='2hsk' size='340' side='right'caption='[[2hsk]]' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[2hsk]] 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=2HSK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HSK FirstGlance]. <br>
-
2HSK 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=2HSK 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=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</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=2hsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hsk OCA], [https://pdbe.org/2hsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hsk RCSB], [https://www.ebi.ac.uk/pdbsum/2hsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hsk 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 lesion]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:06:38 2008''
+

Current revision

NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)

PDB ID 2hsk

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2hsk"
Personal tools