View source for 5vs2


==Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension complex with dTTP bound in Watson-Crick conformation==
<StructureSection load='5vs2' size='340' side='right'caption='[[5vs2]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5vs2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VS2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VS2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5vrx|5vrx]], [[5vry|5vry]], [[5vrz|5vrz]], [[5vs0|5vs0]], [[5vs1|5vs1]], [[5vs4|5vs4]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5vs2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vs2 OCA], [https://pdbe.org/5vs2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vs2 RCSB], [https://www.ebi.ac.uk/pdbsum/5vs2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vs2 ProSAT]</span></td></tr>
</table>
== Function ==
[[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The oxidative DNA lesion 7,8-dihydro-2'-deoxyguanine (8-oxoG) often occurs in double-stranded DNA and poses a threat to genomic integrity due to the ability of 8-oxoG to form stable Watson-Crick base pairs with deoxycytidine (8-oxoG:dC) and Hoogsteen base pairs with deoxyadenosine (8-oxoG:dA). In humans, short-patch base excision repair of 8-oxoG:dA base pairs requires human DNA polymerase beta (hPolbeta) to bypass 8-oxoG. Previously, we have shown hPolbeta-catalyzed 8-oxoG bypass to exhibit low fidelity and identified a unique stacking interaction between the newly incorporated nucleotide (dCMP or dAMP) and the templating 8-oxoG. The effect of this stacking on the ability of hPolbeta to extend from 8-oxoG during long-patch base excision repair was unknown. Here we report pre-steady-state kinetics and time-dependent crystal structures to demonstrate that extension from both 8-oxoG:dC and 8-oxoG:dA base pairs is 18- to 580-fold less efficient compared to 8-oxoG bypass and that extension from 8-oxoG:dC over 8-oxoG:dA is favored by 15-fold. The overall decrease in efficiency of extension relative to 8-oxoG bypass is due to an alternative nucleotide binding conformation in the precatalytic ternary structures (hPolbeta.DNA.dNTP) for both extension contexts, wherein the incoming nucleotide is bound in either the canonical Watson-Crick base pair or a nonplanar base pair. In addition, the decreased stability of the ternary complex of 8-oxoG:dA extension results in further loss of efficiency when compared to 8-oxoG:dC extension. Therefore, we hypothesize that the inefficient extension from 8-oxoG:dA serves as a newly discovered fidelity checkpoint during base excision repair.

Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.,Reed AJ, Suo Z J Am Chem Soc. 2017 Jul 19;139(28):9684-9690. doi: 10.1021/jacs.7b05048. Epub, 2017 Jul 6. PMID:28682600<ref>PMID:28682600</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 5vs2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Human]]
[[Category: Large Structures]]
[[Category: Reed, A J]]
[[Category: Suo, Z]]
[[Category: 8-oxoguanine]]
[[Category: Ber]]
[[Category: Lyase-dna complex]]
[[Category: Polymerase]]
[[Category: Transferase]]