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1odg

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[[Image:1odg.gif|left|200px]]<br />
 
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<applet load="1odg" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1odg, resolution 2.8&Aring;" />
 
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'''VERY-SHORT-PATCH DNA REPAIR ENDONUCLEASE BOUND TO ITS REACTION PRODUCT SITE'''<br />
 
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==Overview==
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==Very-short-patch DNA repair endonuclease bound to its reaction product site==
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Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising, by deamination of 5-methyl-cytosines in specific regulatory sequences. We, have now determined the structure of the archetypal dcm-Vsr endonuclease, from Escherichia coli bound to the cleaved authentic, hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3', 5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of, a 12mer oligonucleotide into a continuous nicked DNA superhelix. The, structure reveals the presence of a Hoogsteen base pair within the, deaminated recognition sequence and the substantial distortions of the DNA, that accompany Vsr binding to product sites.
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<StructureSection load='1odg' size='340' side='right'caption='[[1odg]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1odg]] 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=1ODG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ODG 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=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1odg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1odg OCA], [https://pdbe.org/1odg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1odg RCSB], [https://www.ebi.ac.uk/pdbsum/1odg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1odg ProSAT]</span></td></tr>
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</table>
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== Function ==
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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/od/1odg_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=1odg 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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Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising by deamination of 5-methyl-cytosines in specific regulatory sequences. We have now determined the structure of the archetypal dcm-Vsr endonuclease from Escherichia coli bound to the cleaved authentic hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3' 5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of a 12mer oligonucleotide into a continuous nicked DNA superhelix. The structure reveals the presence of a Hoogsteen base pair within the deaminated recognition sequence and the substantial distortions of the DNA that accompany Vsr binding to product sites.
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==About this Structure==
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Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.,Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH Nucleic Acids Res. 2003 Mar 15;31(6):1633-9. PMID:12626704<ref>PMID:12626704</ref>
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1ODG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ODG 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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Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix., Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH, Nucleic Acids Res. 2003 Mar 15;31(6):1633-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12626704 12626704]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 1odg" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Brown, T.]]
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[[Category: Bunting, K.A.]]
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[[Category: Headley, A.]]
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[[Category: Pearl, L.H.]]
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[[Category: Roe, S.M.]]
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[[Category: Savva, R.]]
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[[Category: ZN]]
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[[Category: dna repai hydrolase]]
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[[Category: dna repair]]
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[[Category: endonuclease]]
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[[Category: metal-binding]]
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[[Category: nuclease]]
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[[Category: very short patch repair]]
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[[Category: zinc]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 16:50:46 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: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Brown T]]
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[[Category: Bunting KA]]
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[[Category: Headley A]]
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[[Category: Pearl LH]]
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[[Category: Roe SM]]
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[[Category: Savva R]]

Current revision

Very-short-patch DNA repair endonuclease bound to its reaction product site

PDB ID 1odg

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