2nq9

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[[Image:2nq9.png|left|200px]]
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==High resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA==
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<StructureSection load='2nq9' size='340' side='right' caption='[[2nq9]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2nq9]] is a 4 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=2NQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NQ9 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nfo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nq9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nq9 RCSB], [http://www.ebi.ac.uk/pdbsum/2nq9 PDBsum]</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/nq/2nq9_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/chain_selection.php?pdb_ID=2ata 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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Escherichia coli endonuclease IV is an archetype for an abasic or apurinic-apyrimidinic endonuclease superfamily crucial for DNA base excision repair. Here biochemical, mutational and crystallographic characterizations reveal a three-metal ion mechanism for damage binding and incision. The 1.10-A resolution DNA-free and the 2.45-A resolution DNA-substrate complex structures capture substrate stabilization by Arg37 and reveal a distorted Zn3-ligand arrangement that reverts, after catalysis, to an ideal geometry suitable to hold rather than release cleaved DNA product. The 1.45-A resolution DNA-product complex structure shows how Tyr72 caps the active site, tunes its dielectric environment and promotes catalysis by Glu261-activated hydroxide, bound to two Zn2+ ions throughout catalysis. These structural, mutagenesis and biochemical results suggest general requirements for abasic site removal in contrast to features specific to the distinct endonuclease IV alpha-beta triose phosphate isomerase (TIM) barrel and APE1 four-layer alpha-beta folds of the apurinic-apyrimidinic endonuclease families.
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{{STRUCTURE_2nq9| PDB=2nq9 | SCENE= }}
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DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.,Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA Nat Struct Mol Biol. 2008 May;15(5):515-22. Epub 2008 Apr 13. PMID:18408731<ref>PMID:18408731</ref>
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===High resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_18408731}}
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==About this Structure==
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[[2nq9]] is a 4 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=2NQ9 OCA].
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==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease|Endonuclease]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:018408731</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Garcin-Hosfield, E D.]]
[[Category: Garcin-Hosfield, E D.]]

Revision as of 04:46, 29 September 2014

High resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA

2nq9, resolution 1.45Å

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OCA

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