1b60

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[[Image:1b60.gif|left|200px]]
[[Image:1b60.gif|left|200px]]
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{{Structure
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|PDB= 1b60 |SIZE=350|CAPTION= <scene name='initialview01'>1b60</scene>
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The line below this paragraph, containing "STRUCTURE_1b60", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=EDC:N3,N4-ETHENO-2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>EDC</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|GENE=
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{{STRUCTURE_1b60| PDB=1b60 | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b60 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b60 OCA], [http://www.ebi.ac.uk/pdbsum/1b60 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b60 RCSB]</span>
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'''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS'''
'''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS'''
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==About this Structure==
==About this Structure==
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1B60 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=1B60 OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B60 OCA].
==Reference==
==Reference==
Solution structure of an 11-mer duplex containing the 3, N(4)-ethenocytosine adduct opposite 2'-deoxycytidine: implications for the recognition of exocyclic lesions by DNA glycosylases., Cullinan D, Johnson F, de los Santos C, J Mol Biol. 2000 Feb 25;296(3):851-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10677286 10677286]
Solution structure of an 11-mer duplex containing the 3, N(4)-ethenocytosine adduct opposite 2'-deoxycytidine: implications for the recognition of exocyclic lesions by DNA glycosylases., Cullinan D, Johnson F, de los Santos C, J Mol Biol. 2000 Feb 25;296(3):851-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10677286 10677286]
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[[Category: Protein complex]]
 
[[Category: Cullinan, D.]]
[[Category: Cullinan, D.]]
[[Category: Johnson, F.]]
[[Category: Johnson, F.]]
[[Category: Santos, C De Los.]]
[[Category: Santos, C De Los.]]
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[[Category: edc]]
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[[Category: Edc]]
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[[Category: ethenodc]]
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[[Category: Ethenodc]]
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[[Category: exocyclic lesion]]
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[[Category: Exocyclic lesion]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 11:06:52 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:54:18 2008''
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Revision as of 08:06, 2 May 2008

Image:1b60.gif

Template:STRUCTURE 1b60

3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS


Overview

Lipid peroxidation products, as well as the metabolic products of vinyl chloride, react with cellular DNA producing the mutagenic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilondC), along with several other exocyclic derivatives. High-resolution NMR spectroscopy and restrained molecular dynamics simulations were used to establish the solution structure of an 11-mer duplex containing an epsilondC.dC base-pair at its center. The NMR data suggested a regular right-handed helical structure having all residues in the anti orientation around the glycosydic torsion angle and Watson-Crick alignments for all canonical base-pairs of the duplex. Restrained molecular dynamics generated a three-dimensional model in excellent agreement with the spectroscopic data. The (epsilondC. dC)-duplex structure is a regular right-handed helix with a slight bend at the lesion site and no severe distortions of the sugar-phosphate backbone. The epsilondC adduct and its partner dC were displaced towards opposite grooves of the helix, resulting in a lesion-containing base-pair that was highly sheared but stabilized to some degree by the formation of a single hydrogen bond. Such a sheared base-pair alignment at the lesion site was previously observed for epsilondC.dG and epsilondC.T duplexes, and was also present in the crystal structures of duplexes containing dG.T and dG. U mismatches. These observations suggest the existence of a substrate structural motif that may be recognized by specific DNA glycosylases during the process of base excision repair.

About this Structure

Full crystallographic information is available from OCA.

Reference

Solution structure of an 11-mer duplex containing the 3, N(4)-ethenocytosine adduct opposite 2'-deoxycytidine: implications for the recognition of exocyclic lesions by DNA glycosylases., Cullinan D, Johnson F, de los Santos C, J Mol Biol. 2000 Feb 25;296(3):851-61. PMID:10677286 Page seeded by OCA on Fri May 2 11:06:52 2008

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