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1tva

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(New page: 200px<br /> <applet load="1tva" size="450" color="white" frame="true" align="right" spinBox="true" caption="1tva, resolution 2.60&Aring;" /> '''HUMAN DNA POLYMERAS...)
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[[Image:1tva.gif|left|200px]]<br />
 
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<applet load="1tva" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1tva, resolution 2.60&Aring;" />
 
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'''HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE THYMIDINE 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 THYMIDINE 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='1tva' size='340' side='right'caption='[[1tva]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1tva]] 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=1TVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TVA 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]] 2.6&#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=1tva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tva OCA], [https://pdbe.org/1tva PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tva RCSB], [https://www.ebi.ac.uk/pdbsum/1tva PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tva 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/1tva_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=1tva ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1TVA 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 NA, MG 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=1TVA OCA].
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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==Reference==
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<references/>
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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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__TOC__
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[[Category: DNA-directed DNA polymerase]]
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Beard, W.A.]]
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[[Category: Beard WA]]
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[[Category: Krahn, J.M.]]
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[[Category: Krahn JM]]
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[[Category: Wilson, S.H.]]
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[[Category: Wilson SH]]
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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 19:28:25 2007''
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Current revision

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

PDB ID 1tva

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