2nqj: Difference between revisions

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{{Seed}}
[[Image:2nqj.png|left|200px]]


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==Crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant bound to damaged DNA==
The line below this paragraph, containing "STRUCTURE_2nqj", creates the "Structure Box" on the page.
<StructureSection load='2nqj' size='340' side='right'caption='[[2nqj]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2nqj]] is a 4 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=2NQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NQJ FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#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=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_2nqj|  PDB=2nqj  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nqj OCA], [https://pdbe.org/2nqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nqj RCSB], [https://www.ebi.ac.uk/pdbsum/2nqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nqj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/END4_ECOLI END4_ECOLI] Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nq/2nqj_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </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/main_output.php?pdb_ID=2nqj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===Crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant bound to damaged DNA===
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2nqj" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18408731}}, adds the Publication Abstract to the page
*[[Apurinic/apyrimidinic endonuclease 3D structures|Apurinic/apyrimidinic endonuclease 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18408731 is the PubMed ID number.
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-->
== References ==
{{ABSTRACT_PUBMED_18408731}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
2NQJ is a 4 chains 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=2NQJ OCA].
 
==Reference==
<ref group="xtra">PMID:18408731</ref><references group="xtra"/>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Garcin-Hosfield, E D.]]
[[Category: Large Structures]]
[[Category: Hosfield, D J.]]
[[Category: Garcin-Hosfield ED]]
[[Category: Tainer, J A.]]
[[Category: Hosfield DJ]]
[[Category: Hydrolase]]
[[Category: Tainer JA]]
[[Category: Tim_barrel]]
[[Category: Trinuclear zinc site]]
 
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Retrieved from "https://proteopedia.org/2nqj"