View source for 3taf


==5-fluorocytosine paired with ddGMP in RB69 gp43==
<StructureSection load='3taf' size='340' side='right'caption='[[3taf]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3taf]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TAF FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C37:5-FLUORO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C37</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3taf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3taf OCA], [https://pdbe.org/3taf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3taf RCSB], [https://www.ebi.ac.uk/pdbsum/3taf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3taf ProSAT]</span></td></tr>
</table>
== Function ==
[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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== Publication Abstract from PubMed ==
5-Hydroxycytosine (5-OHC) is a stable oxidation product of cytosine associated with an increased frequency of C --&gt; T transition mutations. When this lesion escapes recognition by the base excision repair pathway and persists to serve as a templating base during DNA synthesis, replicative DNA polymerases often misincorporate dAMP at the primer terminus, which can lead to fixation of mutations and subsequent disease. To characterize the dynamics of DNA synthesis opposite 5-OHC, we initiated a comparison of unmodified dCMP to 5-OHC, 5-fluorocytosine (5-FC), and 5-methylcytosine (5-MEC) in which these bases act as templates in the active site of RB69 gp43, a high-fidelity DNA polymerase sharing homology with human replicative DNA polymerases. This study presents the first crystal structure of any DNA polymerase binding this physiologically important premutagenic DNA lesion, showing that while dGMP is stabilized by 5-OHC through normal Watson-Crick base pairing, incorporation of dAMP leads to unstacking and instability in the template. Furthermore, the electronegativity of the C5 substituent appears to be important in the miscoding potential of these cytosine-like templates. While dAMP is incorporated opposite 5-OHC approximately 5 times more efficiently than opposite unmodified dCMP, an elevated level of incorporation is also observed opposite 5-FC but not 5-MEC. Taken together, these data imply that the nonuniform templating by 5-OHC is due to weakened stacking capabilities, which allows dAMP incorporation to proceed in a manner similar to that observed opposite abasic sites.

The Miscoding Potential of 5-Hydroxycytosine Arises Due to Template Instability in the Replicative Polymerase Active Site.,Zahn KE, Averill A, Wallace SS, Doublie S Biochemistry. 2011 Nov 3. PMID:22026756<ref>PMID:22026756</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 3taf" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia phage RB69]]
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Zahn KE]]