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[[Image:1oup.gif|left|200px]]
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{{STRUCTURE_1oup|  PDB=1oup  |  SCENE=  }}
'''Crystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA'''


==Crystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA==
<StructureSection load='1oup' size='340' side='right'caption='[[1oup]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1oup]] is a 7 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=1OUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OUP FirstGlance]. <br>
</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>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1oup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oup OCA], [https://pdbe.org/1oup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oup RCSB], [https://www.ebi.ac.uk/pdbsum/1oup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oup ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q7MHK3_VIBVY Q7MHK3_VIBVY]
== 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/ou/1oup_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1oup ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
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:12881435<ref>PMID:12881435</ref>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1OUP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OUP OCA].
</div>
<div class="pdbe-citations 1oup" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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://www.ncbi.nlm.nih.gov/pubmed/12881435 12881435]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
[[Category: Single protein]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Vibrio vulnificus]]
[[Category: Vibrio vulnificus]]
[[Category: Li, C L.]]
[[Category: Li C-L]]
[[Category: Yuan, H S.]]
[[Category: Yuan HS]]
[[Category: Beta-beta-alpha metal motif]]
[[Category: Non-specific endonuclease]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 30 13:55:06 2008''

Latest revision as of 07:10, 30 October 2024

Crystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA

1oup, resolution 2.30Å

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