4fs2: Difference between revisions

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-[[Image:4fs2.png|left|200px]]
+==Base pairing mechanism of N2,3-ethenoguanine with dCTP by human polymerase iota==
+<StructureSection load='4fs2' size='340' side='right' caption='[[4fs2]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4fs2]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FS2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FS2 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=EFG:1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZO[2,1-B]PURIN-4(5H)-ONE'>EFG</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3osn|3osn]], [[3v6h|3v6h]], [[3v6j|3v6j]], [[3v6k|3v6k]], [[4fs1|4fs1]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLI, RAD30B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4fs2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fs2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fs2 RCSB], [http://www.ebi.ac.uk/pdbsum/4fs2 PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+N2,3-Ethenoguanine (N2,3-epsilonG) is one of the exocyclic DNA adducts produced by endogenous processes (e.g., lipid peroxidation) and exposure to bioactivated vinyl monomers such as vinyl chloride, which is a known human carcinogen. Existing studies exploring the miscoding potential of this lesion are quite indirect due to the lability of the glycosidic bond. We utilized a 2'-fluoro isostere approach to stabilize this lesion and synthesized oligonucleotides containing 2'-fluoro-N2,3-epsilon-2'-deoxyarabinoguanosine to investigate the miscoding potential of N2,3-epsilonG by Y-family human DNA polymerases (pols). In primer extension assays, pol eta and pol kappa replicated through N2,3-epsilonG, whereas pol iota and REV1 yielded only one-base incorporation. Steady-state kinetics revealed that dCTP incorporation is preferred opposite N2,3-epsilonG, with relative efficiencies in the order of pol kappa &gt; REV1 &gt; pol eta approximately pol iota, and dTTP misincorporation is the major miscoding event by all four Y-family human DNA pols. Pol iota had the highest dTTP misincorporation frequency (0.71), followed by pol eta (0.63). REV1 misincorporated dTTP and dGTP with much lower frequencies. Crystal structures of pol iota with N2,3-epsilonG paired to dCTP and dTTP revealed Hoogsteen-like base pairing mechanisms. Two hydrogen bonds were observed in the N2,3-epsilonG:dCTP base pair, whereas only one appears to be present in the case of the N2,3-epsilonG:dTTP pair. Base pairing mechanisms derived from the crystal structures explain the slightly favored dCTP insertion for pol iota in steady-state kinetic analysis. Taken together, these results provide a basis for the mutagenic potential of N2,3-epsilonG.
-{{STRUCTURE_4fs2|  PDB=4fs2  |  SCENE=  }}
+Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases.,Zhao L, Pence MG, Christov PP, Wawrzak Z, Choi JY, Rizzo CJ, Egli M, Guengerich FP J Biol Chem. 2012 Aug 21. PMID:22910910<ref>PMID:22910910</ref>
-===Base pairing mechanism of N2,3-ethenoguanine with dCTP by human polymerase iota===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_22910910}}
+==See Also==
+*[[DNA polymerase|DNA polymerase]]
-==About this Structure==
+== References ==
-[[4fs2]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FS2 OCA].
+<references/>
+__TOC__
+</StructureSection>
 [[Category: DNA-directed DNA polymerase]]
 [[Category: Homo sapiens]]
-[[Category: Zhao, L.]]
+[[Category: Zhao, L]]
 [[Category: 2'-fluoro arabinose]]
 [[Category: 3-ethenoguanine]]