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1k3w

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{{STRUCTURE_1k3w| PDB=1k3w | SCENE= }}
 
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===Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA===
 
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{{ABSTRACT_PUBMED_11847126}}
 
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==About this Structure==
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==Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA==
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[[1k3w]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3W OCA].
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<StructureSection load='1k3w' size='340' side='right'caption='[[1k3w]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1k3w]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K3W 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]] 1.42&#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=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1k3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3w OCA], [https://pdbe.org/1k3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k3w RCSB], [https://www.ebi.ac.uk/pdbsum/1k3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k3w ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/END8_ECOLI END8_ECOLI] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. Acts on DNA bubble and 3'-fork structures, suggesting a role in replication-associated DNA repair. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates.<ref>PMID:20031487</ref>
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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/k3/1k3w_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=1k3w ConSurf].
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<div style="clear:both"></div>
==See Also==
==See Also==
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*[[DNA glycosylate|DNA glycosylate]]
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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*[[DNA repair protein human endonuclease VIII-like 1 (NEIL1)|DNA repair protein human endonuclease VIII-like 1 (NEIL1)]]
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== References ==
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*[[Endonuclease|Endonuclease]]
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<references/>
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*[[Fpg Nei Protein Family|Fpg Nei Protein Family]]
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__TOC__
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*[[Fpg Nei Protein Superfamily|Fpg Nei Protein Superfamily]]
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:011847126</ref><references group="xtra"/>
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Fernandes, A S.]]
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[[Category: Large Structures]]
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[[Category: Gerchman, S E.]]
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[[Category: Fernandes AS]]
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[[Category: Gilboa, R.]]
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[[Category: Gerchman SE]]
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[[Category: Golan, G.]]
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[[Category: Gilboa R]]
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[[Category: Grollman, A P.]]
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[[Category: Golan G]]
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[[Category: Kycia, J H.]]
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[[Category: Grollman AP]]
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[[Category: Rieger, R A.]]
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[[Category: Kycia JH]]
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[[Category: Shoham, G.]]
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[[Category: Rieger RA]]
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[[Category: Zharkov, D O.]]
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[[Category: Shoham G]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Zharkov DO]]
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[[Category: Hydrolase/dna]]
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Current revision

Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA

PDB ID 1k3w

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