2vld

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[[Image:2vld.png|left|200px]]
 
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==crystal structure of a repair endonuclease from Pyrococcus abyssi==
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The line below this paragraph, containing "STRUCTURE_2vld", creates the "Structure Box" on the page.
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<StructureSection load='2vld' size='340' side='right'caption='[[2vld]], [[Resolution|resolution]] 2.60&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'>[[2vld]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VLD 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]] 2.6&#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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_2vld| PDB=2vld | 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=2vld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vld OCA], [https://pdbe.org/2vld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vld RCSB], [https://www.ebi.ac.uk/pdbsum/2vld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vld ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NUCS_PYRAB NUCS_PYRAB] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures. Binds to ssDNA.[HAMAP-Rule:MF_00722]<ref>PMID:19609302</ref> <ref>PMID:22431731</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/vl/2vld_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2vld 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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We show that Pyrococcus abyssi PAB2263 (dubbed NucS (nuclease for ss DNA) is a novel archaeal endonuclease that interacts with the replication clamp PCNA. Structural determination of P. abyssi NucS revealed a two-domain dumbbell-like structure that in overall does not resemble any known protein structure. Biochemical and structural studies indicate that NucS orthologues use a non-catalytic ssDNA-binding domain to regulate the cleavage activity at another site, thus resulting into the specific cleavage at double-stranded DNA (dsDNA)/ssDNA junctions on branched DNA substrates. Both 3' and 5' extremities of the ssDNA can be cleaved at the nuclease channel that is too narrow to accommodate duplex DNA. Altogether, our data suggest that NucS proteins constitute a new family of structure-specific DNA endonucleases that are widely distributed in archaea and in bacteria, including Mycobacterium tuberculosis.
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===CRYSTAL STRUCTURE OF A REPAIR ENDONUCLEASE FROM PYROCOCCUS ABYSSI===
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Structure and function of a novel endonuclease acting on branched DNA substrates.,Ren B, Kuhn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, Flament D, Ladenstein R, Myllykallio H EMBO J. 2009 Aug 19;28(16):2479-89. Epub 2009 Jul 16. PMID:19609302<ref>PMID:19609302</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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The line below this paragraph, {{ABSTRACT_PUBMED_19609302}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2vld" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19609302 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19609302}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[2vld]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLD OCA].
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==Reference==
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<ref group="xtra">PMID:019609302</ref><references group="xtra"/>
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[[Category: Pyrococcus abyssi]]
[[Category: Pyrococcus abyssi]]
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[[Category: Briffotaux, J.]]
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[[Category: Briffotaux J]]
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[[Category: Flament, D.]]
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[[Category: Flament D]]
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[[Category: Kuhn, J.]]
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[[Category: Kuhn J]]
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[[Category: Ladenstein, R.]]
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[[Category: Ladenstein R]]
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[[Category: Lavigne, R.]]
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[[Category: Lavigne R]]
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[[Category: Meslet-Cladiere, L.]]
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[[Category: Meslet-Cladiere L]]
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[[Category: Myllykallio, H.]]
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[[Category: Myllykallio H]]
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[[Category: Norais, C.]]
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[[Category: Norais C]]
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[[Category: Ren, B.]]
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[[Category: Ren B]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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Current revision

crystal structure of a repair endonuclease from Pyrococcus abyssi

PDB ID 2vld

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OCA

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