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[[Image:2ivh.gif|left|200px]]
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{{STRUCTURE_2ivh|  PDB=2ivh  |  SCENE=  }}
'''CRYSTAL STRUCTURE OF THE NUCLEASE DOMAIN OF COLE7 (H545Q MUTANT) IN COMPLEX WITH AN 18-BP DUPLEX DNA'''


==Crystal structure of the nuclease domain of ColE7 (H545Q mutant) in complex with an 18-bp duplex DNA==
<StructureSection load='2ivh' size='340' side='right'caption='[[2ivh]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ivh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IVH 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]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2ivh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ivh OCA], [https://pdbe.org/2ivh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ivh RCSB], [https://www.ebi.ac.uk/pdbsum/2ivh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ivh ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CEA7_ECOLX CEA7_ECOLX] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity.  Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.
== 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/iv/2ivh_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=2ivh ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3'O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the 'preferred complex' of the nuclease domain of ColE7 bound to an 18 bp DNA with a thymine before the scissile phosphate had a more distorted DNA phosphate backbone than the backbones in the non-preferred complexes, so that the scissile phosphate was compositionally closer to the endonuclease active site resulting in more efficient DNA cleavage. On the other hand, in the crystal structure of Vvn in complex with a 16 bp DNA, the DNA phosphate backbone was similar and not distorted in comparison with that of a previously reported complex of Vvn with a different DNA sequence. Taken together these results suggest a general structural basis for the sequence-dependent DNA cleavage catalyzed by nonspecific endonucleases, indicating that nonspecific nucleases could induce DNA to deform to distinctive levels depending on the local sequence leading to different cleavage rates along the DNA chain.


==Overview==
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.,Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS Nucleic Acids Res. 2007;35(2):584-94. Epub 2006 Dec 15. PMID:17175542<ref>PMID:17175542</ref>
Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3'O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the 'preferred complex' of the nuclease domain of ColE7 bound to an 18 bp DNA with a thymine before the scissile phosphate had a more distorted DNA phosphate backbone than the backbones in the non-preferred complexes, so that the scissile phosphate was compositionally closer to the endonuclease active site resulting in more efficient DNA cleavage. On the other hand, in the crystal structure of Vvn in complex with a 16 bp DNA, the DNA phosphate backbone was similar and not distorted in comparison with that of a previously reported complex of Vvn with a different DNA sequence. Taken together these results suggest a general structural basis for the sequence-dependent DNA cleavage catalyzed by nonspecific endonucleases, indicating that nonspecific nucleases could induce DNA to deform to distinctive levels depending on the local sequence leading to different cleavage rates along the DNA chain.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2IVH is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVH OCA].
</div>
<div class="pdbe-citations 2ivh" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases., Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS, Nucleic Acids Res. 2007;35(2):584-94. Epub 2006 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17175542 17175542]
*[[Colicin 3D structures|Colicin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Doudeva, L G.]]
[[Category: Doudeva LG]]
[[Category: Li, C L.]]
[[Category: Li CL]]
[[Category: Wang, Y T.]]
[[Category: Wang YT]]
[[Category: Yang, W J.]]
[[Category: Yang WJ]]
[[Category: Yuan, H S.]]
[[Category: Yuan HS]]
[[Category: Antibiotic]]
[[Category: Antimicrobial]]
[[Category: Bacteriocin]]
[[Category: Endonuclease]]
[[Category: Hydrolase]]
[[Category: Hydrolase/dna complex]]
[[Category: Metal-binding]]
[[Category: Nuclease]]
[[Category: Plasmid]]
[[Category: Zinc]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:56:20 2008''
Retrieved from "https://proteopedia.org/2ivh"