2hsk: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2hsk.gif|left|200px]]


{{Structure
==NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)==
|PDB= 2hsk |SIZE=350|CAPTION= <scene name='initialview01'>2hsk</scene>
<StructureSection load='2hsk' size='340' side='right'caption='[[2hsk]]' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<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>
|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=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</scene></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=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>
 
</table>
'''NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Synthetic construct]]
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: Case DA]]
 
[[Category: Chen J]]
==About this Structure==
[[Category: Dupradeau FY]]
2HSK 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=2HSK OCA].  
[[Category: Stubbe J]]
 
[[Category: Turner CJ]]
==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 lesion]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:21:04 2008''

Latest revision as of 06:41, 1 May 2024

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

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=2hsk&oldid=4135534"