2dy4

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[[Image:2dy4.gif|left|200px]]
 
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{{Structure
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==Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol==
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|PDB= 2dy4 |SIZE=350|CAPTION= <scene name='initialview01'>2dy4</scene>, resolution 2.650&Aring;
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<StructureSection load='2dy4' size='340' side='right'caption='[[2dy4]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CTG:(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5&#39;-MONOPHOSPHATE'>CTG</scene>, <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=MSE:SELENOMETHIONINE'>MSE</scene>
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<table><tr><td colspan='2'>[[2dy4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DY4 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span>
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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]] 2.65&#8491;</td></tr>
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|GENE= gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTG:(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5-MONOPHOSPHATE'>CTG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=2dy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy4 OCA], [https://pdbe.org/2dy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dy4 RCSB], [https://www.ebi.ac.uk/pdbsum/2dy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dy4 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1clq|1CLQ]], [[1ig9|1IG9]], [[1rv2|1RV2]], [[1q9x|1Q9X]], [[1q9y|1Q9Y]], [[2dtu|2DTU]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dy4 OCA], [http://www.ebi.ac.uk/pdbsum/2dy4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dy4 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
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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/dy/2dy4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2dy4 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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Thymine glycol (Tg) is a common product of oxidation and ionizing radiation, including that used for cancer treatment. Although Tg is a poor mutagenic lesion, it has been shown to present a strong block to both repair and replicative DNA polymerases. The 2.65-A crystal structure of a binary complex of the replicative RB69 DNA polymerase with DNA shows that the templating Tg is intrahelical and forms a regular Watson-Crick base pair with the incorporated A. The C5 methyl group protrudes axially from the ring of the damaged pyrimidine and hinders stacking of the adjacent 5' template guanine. The position of the displaced 5' template guanine is such that the next incoming nucleotide cannot be incorporated into the growing primer strand, and it explains why primer extension past the lesion is prohibited even though DNA polymerases can readily incorporate an A across from the Tg lesion.
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'''Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol'''
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A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.,Aller P, Rould MA, Hogg M, Wallace SS, Doublie S Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):814-8. Epub 2007 Jan 8. PMID:17210917<ref>PMID:17210917</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 2dy4" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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2DY4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DY4 OCA].
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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[[Category: DNA-directed DNA polymerase]]
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== References ==
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[[Category: Enterobacteria phage rb69]]
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<references/>
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[[Category: Single protein]]
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__TOC__
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[[Category: Aller, P.]]
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</StructureSection>
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[[Category: Doublie, S.]]
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[[Category: Escherichia phage RB69]]
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[[Category: Hogg, M.]]
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[[Category: Large Structures]]
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[[Category: Rould, M A.]]
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[[Category: Aller P]]
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[[Category: Wallace, S S.]]
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[[Category: Doublie S]]
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[[Category: dna lesion]]
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[[Category: Hogg M]]
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[[Category: dna polymerase]]
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[[Category: Rould MA]]
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[[Category: oxidative thymine lesion]]
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[[Category: Wallace SS]]
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[[Category: thymine glycol]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:41:09 2008''
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Current revision

Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol

PDB ID 2dy4

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