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2vld
From Proteopedia
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| - | [[Image:2vld.png|left|200px]] | ||
| - | < | + | ==crystal structure of a repair endonuclease from Pyrococcus abyssi== |
| - | + | <StructureSection load='2vld' size='340' side='right'caption='[[2vld]], [[Resolution|resolution]] 2.60Å' scene=''> | |
| - | You may | + | == Structural highlights == |
| - | + | <table><tr><td colspan='2'>[[2vld]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. 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> | |
| - | + | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |
| - | - | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nucS, PYRAB01260, PAB2263 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</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=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> | |
| + | </table> | ||
| + | == Function == | ||
| + | [[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> | ||
| + | == 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/vl/2vld_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=2vld ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| - | + | 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> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2vld" style="background-color:#fffaf0;"></div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | == | + | [[Category: Pyrococcus abyssi erauso et al. 1993]] |
| - | + | [[Category: Large Structures]] | |
| - | + | [[Category: Briffotaux, J]] | |
| - | == | + | [[Category: Flament, D]] |
| - | < | + | [[Category: Kuhn, J]] |
| - | [[Category: Pyrococcus abyssi]] | + | [[Category: Ladenstein, R]] |
| - | [[Category: Briffotaux, J | + | [[Category: Lavigne, R]] |
| - | [[Category: Flament, D | + | [[Category: Meslet-Cladiere, L]] |
| - | [[Category: Kuhn, J | + | [[Category: Myllykallio, H]] |
| - | [[Category: Ladenstein, R | + | [[Category: Norais, C]] |
| - | [[Category: Lavigne, R | + | [[Category: Ren, B]] |
| - | [[Category: Meslet-Cladiere, L | + | |
| - | [[Category: Myllykallio, H | + | |
| - | [[Category: Norais, C | + | |
| - | [[Category: Ren, B | + | |
[[Category: Endonuclease]] | [[Category: Endonuclease]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
Current revision
crystal structure of a repair endonuclease from Pyrococcus abyssi
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