2ea0: Difference between revisions
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==Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in complex with AP-site containing DNA substrate== | ==Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in complex with AP-site containing DNA substrate== | ||
<StructureSection load='2ea0' size='340' side='right' caption='[[2ea0]], [[Resolution|resolution]] 1.40Å' scene=''> | <StructureSection load='2ea0' size='340' side='right'caption='[[2ea0]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2ea0]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2ea0]] 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=2EA0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EA0 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ea0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ea0 OCA], [https://pdbe.org/2ea0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ea0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ea0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ea0 ProSAT]</span></td></tr> | |||
</table> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | == Function == | ||
<table> | [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> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ea/2ea0_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ea/2ea0_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</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/ | </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=2ea0 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
==See Also== | ==See Also== | ||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
*[[Endonuclease|Endonuclease]] | == References == | ||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Golan G]] | ||
[[Category: Grollman AP]] | |||
[[Category: | [[Category: Shoham G]] | ||
[[Category: | [[Category: Zharov DO]] | ||
[[Category: | |||