1tv9

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(New page: 200px<br /> <applet load="1tv9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1tv9, resolution 2.00&Aring;" /> '''HUMAN DNA POLYMERAS...)
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[[Image:1tv9.gif|left|200px]]<br />
 
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<applet load="1tv9" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1tv9, resolution 2.00&Aring;" />
 
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'''HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE ADENINE AND INCOMING CYTIDINE'''<br />
 
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==Overview==
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==HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE ADENINE AND INCOMING CYTIDINE==
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DNA polymerases generally select the correct nucleotide from a pool of, structurally similar molecules to preserve Watson-Crick base-pairing, rules. We report the structure of DNA polymerase beta with DNA mismatches, situated in the polymerase active site. This was achieved by using nicked, product DNA that traps the mispair (template-primer, A-C or T-C) in the, nascent base pair binding pocket. The structure of each mispair complex, indicates that the bases do not form hydrogen bonds with one another, but, form a staggered arrangement where the bases of the mispair partially, overlap. This prevents closure/opening of the N subdomain that is believed, to be required for catalytic cycling. The partially open conformation of, the N subdomain results in distinct hydrogen bonding networks that are, unique for each mispair. These structures define diverse molecular aspects, of misinsertion that are consistent with the induced-fit model for, substrate specificity.
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<StructureSection load='1tv9' size='340' side='right'caption='[[1tv9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1tv9]] 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=1TV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TV9 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&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1tv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tv9 OCA], [https://pdbe.org/1tv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tv9 RCSB], [https://www.ebi.ac.uk/pdbsum/1tv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tv9 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/tv/1tv9_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=1tv9 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 generally select the correct nucleotide from a pool of structurally similar molecules to preserve Watson-Crick base-pairing rules. We report the structure of DNA polymerase beta with DNA mismatches situated in the polymerase active site. This was achieved by using nicked product DNA that traps the mispair (template-primer, A-C or T-C) in the nascent base pair binding pocket. The structure of each mispair complex indicates that the bases do not form hydrogen bonds with one another, but form a staggered arrangement where the bases of the mispair partially overlap. This prevents closure/opening of the N subdomain that is believed to be required for catalytic cycling. The partially open conformation of the N subdomain results in distinct hydrogen bonding networks that are unique for each mispair. These structures define diverse molecular aspects of misinsertion that are consistent with the induced-fit model for substrate specificity.
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==About this Structure==
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Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity.,Krahn JM, Beard WA, Wilson SH Structure. 2004 Oct;12(10):1823-32. PMID:15458631<ref>PMID:15458631</ref>
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1TV9 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 PO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TV9 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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Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity., Krahn JM, Beard WA, Wilson SH, Structure. 2004 Oct;12(10):1823-32. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15458631 15458631]
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</div>
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[[Category: DNA-directed DNA polymerase]]
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<div class="pdbe-citations 1tv9" style="background-color:#fffaf0;"></div>
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[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Beard, W.M.]]
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[[Category: Krahn, J.M.]]
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[[Category: Wilson, S.H.]]
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[[Category: MG]]
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[[Category: NA]]
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[[Category: PO4]]
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[[Category: base excision repair]]
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[[Category: dna mismatch]]
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[[Category: dna repair]]
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[[Category: nucleotidyltransferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 19:28:22 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: Beard WM]]
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[[Category: Krahn JM]]
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[[Category: Wilson SH]]

Current revision

HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE ADENINE AND INCOMING CYTIDINE

PDB ID 1tv9

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