2bgw

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[[Image:2bgw.gif|left|200px]]<br /><applet load="2bgw" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2bgw, resolution 2.80&Aring;" />
 
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'''XPF FROM AEROPYRUM PERNIX, COMPLEX WITH DNA'''<br />
 
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==Overview==
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==XPF from Aeropyrum pernix, complex with DNA==
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The XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA, (dsDNA) within asymmetric branched DNA substrates and play an essential, role in nucleotide excision repair, recombination and genome integrity. We, report the structure of an archaeal XPF homodimer alone and bound to, dsDNA. Superposition of these structures reveals a large domain movement, upon binding DNA, indicating how the (HhH)(2) domain and the nuclease, domain are coupled to allow the recognition of, double-stranded/single-stranded DNA junctions. We identify two, nonequivalent DNA-binding sites and propose a model in which XPF distorts, the 3' flap substrate in order to engage both binding sites and promote, strand cleavage. The model rationalises published biochemical data and, implies a novel role for the ERCC1 subunit of eukaryotic XPF complexes.
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<StructureSection load='2bgw' size='340' side='right'caption='[[2bgw]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2bgw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix] 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=2BGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BGW FirstGlance]. <br>
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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]] 2.8&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=2bgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bgw OCA], [https://pdbe.org/2bgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bgw RCSB], [https://www.ebi.ac.uk/pdbsum/2bgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bgw ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9YC15_AERPE Q9YC15_AERPE]
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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/bg/2bgw_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=2bgw 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 XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA (dsDNA) within asymmetric branched DNA substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. We report the structure of an archaeal XPF homodimer alone and bound to dsDNA. Superposition of these structures reveals a large domain movement upon binding DNA, indicating how the (HhH)(2) domain and the nuclease domain are coupled to allow the recognition of double-stranded/single-stranded DNA junctions. We identify two nonequivalent DNA-binding sites and propose a model in which XPF distorts the 3' flap substrate in order to engage both binding sites and promote strand cleavage. The model rationalises published biochemical data and implies a novel role for the ERCC1 subunit of eukaryotic XPF complexes.
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==About this Structure==
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Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.,Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A, Knowles PP, White MF, McDonald NQ EMBO J. 2005 Mar 9;24(5):895-905. Epub 2005 Feb 17. PMID:15719018<ref>PMID:15719018</ref>
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2BGW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix] with MG and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:So4 Binding Site For Chain D'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BGW OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition., Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A, Knowles PP, White MF, McDonald NQ, EMBO J. 2005 Mar 9;24(5):895-905. Epub 2005 Feb 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15719018 15719018]
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</div>
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[[Category: Aeropyrum pernix]]
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<div class="pdbe-citations 2bgw" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Fadden, A.]]
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[[Category: Knowles, P.]]
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[[Category: Lally, J.]]
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[[Category: Mcdonald, N.Q.]]
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[[Category: Murray-Rust, J.]]
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[[Category: Newman, M.]]
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[[Category: Rudolf, J.]]
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[[Category: White, M.F.]]
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[[Category: MG]]
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[[Category: SO4]]
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[[Category: hydrolase]]
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[[Category: nucleotide excision repair]]
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[[Category: structure specific endonuclease]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 18:46:25 2007''
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Aeropyrum pernix]]
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[[Category: Large Structures]]
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[[Category: Synthetic construct]]
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[[Category: Fadden A]]
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[[Category: Knowles PP]]
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[[Category: Lally J]]
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[[Category: McDonald NQ]]
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[[Category: Murray-Rust J]]
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[[Category: Newman M]]
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[[Category: Rudolf J]]
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[[Category: White MF]]

Current revision

XPF from Aeropyrum pernix, complex with DNA

PDB ID 2bgw

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