2voa

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{{Seed}}
 
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[[Image:2voa.png|left|200px]]
 
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==Structure of an AP Endonuclease from Archaeoglobus fulgidus==
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The line below this paragraph, containing "STRUCTURE_2voa", creates the "Structure Box" on the page.
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<StructureSection load='2voa' size='340' side='right'caption='[[2voa]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2voa]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VOA FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.7&#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=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
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{{STRUCTURE_2voa| PDB=2voa | SCENE= }}
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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=2voa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2voa OCA], [https://pdbe.org/2voa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2voa RCSB], [https://www.ebi.ac.uk/pdbsum/2voa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2voa ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/O29675_ARCFU O29675_ARCFU]
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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/vo/2voa_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=2voa 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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The major AP endonuclease in Escherichia coli Exonuclease III (ExoIII) is frequently used in gene technology due to its strong exonucleolytic activity. A thermostabilized variant of ExoIII or a homologous enzyme from thermophilic organisms could be most useful for further applications. For this purpose we characterized a nuclease from the hyperthermophilic archaeon Archaeoglobus fulgidus (Af_Exo), which shares 33% overall sequence identity and 55% similarity to ExoIII. The gene coding for this thermostable enzyme was cloned and expressed in E. coli. The purified protein shows a strong Mg(2+)-dependent nicking activity at AP-sites, nicking of undamaged double-stranded (ds) DNA and a weak exonucleolytic activity. A V217G variant of the enzyme was crystallized with decamer ds-DNA molecule, and the three-dimensional structure was determined to 1.7A resolution. Besides our goal to find or produce a thermostable exonuclease, the structural and catalytic data of Af_Exo and a series of mutant proteins, based on the crystal structure, provide new insight into the mechanism of abasic site recognition and repair. Each of the hydrophobic residues Phe 200, Trp 215 and Val 217, forming a binding pocket for the abasic deoxyribose in Af_Exo, were mutated to glycine or serine. By expanding the size of the binding pocket the unspecific endonucleolytic activity is increased. Thus, size and flexibility of the mostly hydrophobic binding pocket have a significant influence on AP-site specificity. We suggest that its tight fitting to the flipped-out deoxyribose allows for a preferred competent binding of abasic sites. In a larger or more flexible pocket however, intact nucleotides more easily bind in a catalytically competent conformation, resulting in loss of specificity. Moreover, with mutations of Phe 200 and Trp 215 we induced a strong exonucleolytic activity on undamaged DNA.
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===STRUCTURE OF AN AP ENDONUCLEASE FROM ARCHAEOGLOBUS FULGIDUS===
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Structure and function of the abasic site specificity pocket of an AP endonuclease from Archaeoglobus fulgidus.,Schmiedel R, Kuettner EB, Keim A, Strater N, Greiner-Stoffele T DNA Repair (Amst). 2008 Dec 4. PMID:19015049<ref>PMID:19015049</ref>
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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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<div class="pdbe-citations 2voa" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19015049}}, adds the Publication Abstract to the page
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*[[Exonuclease 3D structures|Exonuclease 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19015049 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19015049}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2VOA is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VOA OCA].
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==Reference==
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<ref group="xtra">PMID:19015049</ref><ref group="xtra">PMID:17142920</ref><references group="xtra"/>
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[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
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[[Category: Greiner-Stoffele, T.]]
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[[Category: Large Structures]]
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[[Category: Kuettner, E B.]]
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[[Category: Synthetic construct]]
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[[Category: Schmiedel, R.]]
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[[Category: Greiner-Stoffele T]]
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[[Category: Strater, N.]]
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[[Category: Kuettner EB]]
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[[Category: Ap endonuclease]]
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[[Category: Schmiedel R]]
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[[Category: Archaeoglobus fulgidus]]
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[[Category: Strater N]]
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[[Category: Exoiii]]
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[[Category: Lyase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:21:29 2010''
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Current revision

Structure of an AP Endonuclease from Archaeoglobus fulgidus

PDB ID 2voa

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