4fs1
From Proteopedia
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4fs1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=4FS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FS1 FirstGlance]. <br> | <table><tr><td colspan='2'>[[4fs1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=4FS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FS1 FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</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=4fs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fs1 OCA], [https://pdbe.org/4fs1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fs1 RCSB], [https://www.ebi.ac.uk/pdbsum/4fs1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fs1 ProSAT]</span></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=4fs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fs1 OCA], [https://pdbe.org/4fs1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fs1 RCSB], [https://www.ebi.ac.uk/pdbsum/4fs1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fs1 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref> | [https://www.uniprot.org/uniprot/POLI_HUMAN POLI_HUMAN] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity.<ref>PMID:11013228</ref> <ref>PMID:11251121</ref> <ref>PMID:11387224</ref> <ref>PMID:12410315</ref> <ref>PMID:14630940</ref> <ref>PMID:15199127</ref> <ref>PMID:15254543</ref> | ||
| - | <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 > REV1 > 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. | ||
| - | + | ==See Also== | |
| - | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |
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== References == | == References == | ||
<references/> | <references/> | ||
Current revision
Base pairing mechanism of N2,3-ethenoguanine with dTTP by human polymerase iota
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