1zjn

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(New page: 200px<br /> <applet load="1zjn" size="450" color="white" frame="true" align="right" spinBox="true" caption="1zjn, resolution 2.61&Aring;" /> '''Human DNA Polymeras...)
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[[Image:1zjn.gif|left|200px]]<br />
 
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<applet load="1zjn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1zjn, resolution 2.61&Aring;" />
 
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'''Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus with dGTP'''<br />
 
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==Overview==
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==Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus with dGTP==
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DNA polymerases occasionally insert the wrong nucleotide. For this error, to become a mutation, the mispair must be extended. We report a structure, of DNA polymerase beta (pol beta) with a DNA mismatch at the boundary of, the polymerase active site. The structure of this complex indicates that, the templating adenine of the mispair stacks with the primer terminus, adenine while the templating (coding) cytosine is flipped out of the DNA, helix. Soaking the crystals of the binary complex with dGTP resulted in, crystals of a ternary substrate complex. In this case, the templating, cytosine is observed within the DNA helix and forms Watson-Crick hydrogen, bonds with the incoming dGTP. The adenine at the primer terminus has, rotated into a syn-conformation to interact with the opposite adenine in a, planar configuration. Yet, the 3'-hydroxyl on the primer terminus is out, of position for efficient nucleotide insertion.
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<StructureSection load='1zjn' size='340' side='right'caption='[[1zjn]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1zjn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZJN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZJN 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]] 2.61&#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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1zjn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zjn OCA], [https://pdbe.org/1zjn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zjn RCSB], [https://www.ebi.ac.uk/pdbsum/1zjn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zjn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
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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/zj/1zjn_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=1zjn 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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DNA polymerases occasionally insert the wrong nucleotide. For this error to become a mutation, the mispair must be extended. We report a structure of DNA polymerase beta (pol beta) with a DNA mismatch at the boundary of the polymerase active site. The structure of this complex indicates that the templating adenine of the mispair stacks with the primer terminus adenine while the templating (coding) cytosine is flipped out of the DNA helix. Soaking the crystals of the binary complex with dGTP resulted in crystals of a ternary substrate complex. In this case, the templating cytosine is observed within the DNA helix and forms Watson-Crick hydrogen bonds with the incoming dGTP. The adenine at the primer terminus has rotated into a syn-conformation to interact with the opposite adenine in a planar configuration. Yet, the 3'-hydroxyl on the primer terminus is out of position for efficient nucleotide insertion.
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==About this Structure==
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Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.,Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH Structure. 2005 Aug;13(8):1225-33. PMID:16084394<ref>PMID:16084394</ref>
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1ZJN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with MG, NA and DGT as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ZJN 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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Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate., Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH, Structure. 2005 Aug;13(8):1225-33. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16084394 16084394]
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</div>
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[[Category: Homo sapiens]]
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<div class="pdbe-citations 1zjn" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Batra, V.K.]]
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[[Category: Beard, W.A.]]
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[[Category: Pedersen, L.C.]]
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[[Category: Shock, D.D.]]
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[[Category: Wilson, S.H.]]
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[[Category: DGT]]
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[[Category: MG]]
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[[Category: NA]]
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[[Category: dna/lyase/transferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 20:35:34 2007''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 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: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Batra VK]]
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[[Category: Beard WA]]
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[[Category: Pedersen LC]]
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[[Category: Shock DD]]
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[[Category: Wilson SH]]

Current revision

Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus with dGTP

PDB ID 1zjn

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