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2oq4

From Proteopedia

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[[Image:2oq4.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate==
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|PDB= 2oq4 |SIZE=350|CAPTION= <scene name='initialview01'>2oq4</scene>, resolution 2.60&Aring;
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<StructureSection load='2oq4' size='340' side='right'caption='[[2oq4]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Ped+Binding+Site+For+Residue+D+427'>AC1</scene>, <scene name='pdbsite=AC2:Ped+Binding+Site+For+Residue+F+427'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Residue+A+501'>AC3</scene>, <scene name='pdbsite=AC4:Zn+Binding+Site+For+Residue+B+501'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+A+601'>AC5</scene>, <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+B+602'>AC6</scene> and <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+B+603'>AC7</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
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<table><tr><td colspan='2'>[[2oq4]] is a 6 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=2OQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OQ4 FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.6&#8491;</td></tr>
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|GENE= Nei ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <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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}}
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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=2oq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oq4 OCA], [https://pdbe.org/2oq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oq4 RCSB], [https://www.ebi.ac.uk/pdbsum/2oq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oq4 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/oq/2oq4_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=2oq4 ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate'''
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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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==About this Structure==
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<references/>
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2OQ4 is a [[Protein complex]] structure of sequences 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=2OQ4 OCA].
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Golan, G.]]
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[[Category: Golan G]]
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[[Category: Grollman, A P.]]
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[[Category: Grollman AP]]
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[[Category: Shoahm, G.]]
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[[Category: Shoahm G]]
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[[Category: Zharkov, D O.]]
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[[Category: Zharkov DO]]
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[[Category: NA]]
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[[Category: SO4]]
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[[Category: ZN]]
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[[Category: base excision]]
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[[Category: covalent intermediate]]
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[[Category: crystal structure]]
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[[Category: dna repair]]
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[[Category: endonuclease viii]]
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[[Category: hydrolase/dna complex]]
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[[Category: oxidative damage]]
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[[Category: reaction mechanism]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:03:00 2008''
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Current revision

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate

PDB ID 2oq4

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