1p59

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(New page: 200px<br /><applet load="1p59" size="450" color="white" frame="true" align="right" spinBox="true" caption="1p59, resolution 2.50&Aring;" /> '''Structure of a non-c...)
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[[Image:1p59.gif|left|200px]]<br /><applet load="1p59" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1p59, resolution 2.50&Aring;" />
 
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'''Structure of a non-covalent Endonuclease III-DNA Complex'''<br />
 
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==Overview==
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==Structure of a non-covalent Endonuclease III-DNA Complex==
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Nearly all cells express proteins that confer resistance to the mutagenic, effects of oxidative DNA damage. The primary defense against the toxicity, of oxidative nucleobase lesions in DNA is the base-excision repair (BER), pathway. Endonuclease III (EndoIII) is a [4Fe-4S] cluster-containing DNA, glycosylase with repair activity specific for oxidized pyrimidine lesions, in duplex DNA. We have determined the crystal structure of a trapped, intermediate that represents EndoIII frozen in the act of repairing DNA., The structure of the protein-DNA complex provides insight into the ability, of EndoIII to recognize and repair a diverse array of oxidatively damaged, bases. This structure also suggests a rationale for the frequent, occurrence in certain human cancers of a specific mutation in the related, DNA repair protein MYH.
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<StructureSection load='1p59' size='340' side='right'caption='[[1p59]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1p59]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P59 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p59 OCA], [https://pdbe.org/1p59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p59 RCSB], [https://www.ebi.ac.uk/pdbsum/1p59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p59 ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p5/1p59_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1p59 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Nearly all cells express proteins that confer resistance to the mutagenic effects of oxidative DNA damage. The primary defense against the toxicity of oxidative nucleobase lesions in DNA is the base-excision repair (BER) pathway. Endonuclease III (EndoIII) is a [4Fe-4S] cluster-containing DNA glycosylase with repair activity specific for oxidized pyrimidine lesions in duplex DNA. We have determined the crystal structure of a trapped intermediate that represents EndoIII frozen in the act of repairing DNA. The structure of the protein-DNA complex provides insight into the ability of EndoIII to recognize and repair a diverse array of oxidatively damaged bases. This structure also suggests a rationale for the frequent occurrence in certain human cancers of a specific mutation in the related DNA repair protein MYH.
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==About this Structure==
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Structure of a trapped endonuclease III-DNA covalent intermediate.,Fromme JC, Verdine GL EMBO J. 2003 Jul 1;22(13):3461-71. PMID:12840008<ref>PMID:12840008</ref>
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1P59 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with NA and SF4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1P59 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure of a trapped endonuclease III-DNA covalent intermediate., Fromme JC, Verdine GL, EMBO J. 2003 Jul 1;22(13):3461-71. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12840008 12840008]
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</div>
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[[Category: Geobacillus stearothermophilus]]
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<div class="pdbe-citations 1p59" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Fromme, J.C.]]
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[[Category: Verdine, G.L.]]
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[[Category: NA]]
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[[Category: SF4]]
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[[Category: [4fe-4s] cluster]]
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[[Category: dna glycosylase]]
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[[Category: dna repair]]
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[[Category: iron-sulfur cluster]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:01:01 2007''
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Geobacillus stearothermophilus]]
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[[Category: Large Structures]]
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[[Category: Fromme JC]]
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[[Category: Verdine GL]]

Current revision

Structure of a non-covalent Endonuclease III-DNA Complex

PDB ID 1p59

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