1cw0

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[[Image:1cw0.gif|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA==
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|PDB= 1cw0 |SIZE=350|CAPTION= <scene name='initialview01'>1cw0</scene>, resolution 2.30&Aring;
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<StructureSection load='1cw0' size='340' side='right'caption='[[1cw0]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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<table><tr><td colspan='2'>[[1cw0]] is a 4 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=1CW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CW0 FirstGlance]. <br>
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|ACTIVITY=
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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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|GENE=
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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=ZN:ZINC+ION'>ZN</scene></td></tr>
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|DOMAIN=
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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=1cw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cw0 OCA], [https://pdbe.org/1cw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cw0 RCSB], [https://www.ebi.ac.uk/pdbsum/1cw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cw0 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cw0 OCA], [http://www.ebi.ac.uk/pdbsum/1cw0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cw0 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/VSR_ECOLI VSR_ECOLI] Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these mismatches can lead to C-to-C transition mutations. The very short patch (VSP) repair process in E.coli counteracts the mutagenic process by repairing the mismatches in favor of the G-containing strand. This enzyme is an endonuclease that nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue that is mismatched to 2'-deoxyguanosine. The incision is mismatch-dependent and strand-specific.
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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/cw/1cw0_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=1cw0 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 crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli, the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine. Extensive interactions between the DNA and the protein characterize a novel recognition mechanism, where three aromatic residues intercalate from the major groove into the DNA to strikingly deform the base pair stacking. With the presence of a cleaved DNA intermediate in the active center, the structure of the Vsr/DNA complex provides detailed insights into the catalytic mechanism for endonuclease activity.
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'''CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA'''
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Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex.,Tsutakawa SE, Jingami H, Morikawa K Cell. 1999 Dec 10;99(6):615-23. PMID:10612397<ref>PMID:10612397</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1cw0" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli, the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine. Extensive interactions between the DNA and the protein characterize a novel recognition mechanism, where three aromatic residues intercalate from the major groove into the DNA to strikingly deform the base pair stacking. With the presence of a cleaved DNA intermediate in the active center, the structure of the Vsr/DNA complex provides detailed insights into the catalytic mechanism for endonuclease activity.
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1CW0 is a [[Single protein]] structure of sequence 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=1CW0 OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex., Tsutakawa SE, Jingami H, Morikawa K, Cell. 1999 Dec 10;99(6):615-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10612397 10612397]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Jingami, H.]]
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[[Category: Jingami H]]
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[[Category: Morikawa, K.]]
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[[Category: Morikawa K]]
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[[Category: Tsutakawa, S E.]]
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[[Category: Tsutakawa SE]]
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[[Category: hydrolase/dna]]
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[[Category: intercalation]]
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[[Category: mismatch]]
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[[Category: protein-dna complex]]
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[[Category: zinc]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:29:36 2008''
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Current revision

CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA

PDB ID 1cw0

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