1ouo

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[[Image:1ouo.gif|left|200px]]<br /><applet load="1ouo" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ouo, resolution 2.30&Aring;" />
 
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'''Crystal structure of the periplasmic endonuclease Vvn'''<br />
 
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==Overview==
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==Crystal structure of the periplasmic endonuclease Vvn==
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The Vibrio vulnificus nuclease, Vvn, is a non-specific periplasmic nuclease capable of digesting DNA and RNA. The crystal structure of Vvn and that of Vvn mutant H80A in complex with DNA were resolved at 2.3 A resolution. Vvn has a novel mixed alpha/beta topology containing four disulfide bridges, suggesting that Vvn is not active under reducing conditions in the cytoplasm. The overall structure of Vvn shows no similarity to other endonucleases; however, a known 'betabetaalpha-metal' motif is identified in the central cleft region. The crystal structure of the mutant Vvn-DNA complex demonstrates that Vvn binds mainly at the minor groove of DNA, resulting in duplex bending towards the major groove by approximately 20 degrees. Only the DNA phosphate backbones make hydrogen bonds with Vvn, suggesting a structural basis for its sequence-independent recognition of DNA and RNA. Based on the enzyme-substrate and enzyme-product structures observed in the mutant Vvn-DNA crystals, a catalytic mechanism is proposed. This structural study suggests that Vvn hydrolyzes DNA by a general single-metal ion mechanism, and indicates how non-specific DNA-binding proteins may recognize DNA.
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<StructureSection load='1ouo' size='340' side='right'caption='[[1ouo]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ouo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OUO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OUO 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]] 2.3&#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=MSE:SELENOMETHIONINE'>MSE</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=1ouo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ouo OCA], [https://pdbe.org/1ouo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ouo RCSB], [https://www.ebi.ac.uk/pdbsum/1ouo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ouo ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q7MHK3_VIBVY Q7MHK3_VIBVY]
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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/ou/1ouo_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=1ouo ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1OUO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OUO OCA].
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site., Li CL, Hor LI, Chang ZF, Tsai LC, Yang WZ, Yuan HS, EMBO J. 2003 Aug 1;22(15):4014-25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12881435 12881435]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Vibrio vulnificus]]
[[Category: Vibrio vulnificus]]
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[[Category: Li, C L.]]
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[[Category: Li CL]]
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[[Category: Yuan, H S.]]
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[[Category: Yuan HS]]
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[[Category: MG]]
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[[Category: beta-beta-alpha-metal motif]]
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[[Category: non-specific endonuclease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:21:44 2008''
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Current revision

Crystal structure of the periplasmic endonuclease Vvn

PDB ID 1ouo

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