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| | ==Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4== | | ==Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4== |
| - | <StructureSection load='4jv0' size='340' side='right' caption='[[4jv0]], [[Resolution|resolution]] 2.95Å' scene=''> | + | <StructureSection load='4jv0' size='340' side='right'caption='[[4jv0]], [[Resolution|resolution]] 2.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jv0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JV0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jv0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JV0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</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]] 2.95Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KAG:2-DEOXY-N-[(1S)-1-METHYL-3-OXOPROPYL]GUANOSINE+5-PHOSPHATE'>KAG</scene></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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=KAG:2-DEOXY-N-[(1S)-1-METHYL-3-OXOPROPYL]GUANOSINE+5-PHOSPHATE'>KAG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4juz|4juz]], [[4jv1|4jv1]], [[4jv2|4jv2]]</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=4jv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jv0 OCA], [https://pdbe.org/4jv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jv0 RCSB], [https://www.ebi.ac.uk/pdbsum/4jv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jv0 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=4jv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jv0 OCA], [http://pdbe.org/4jv0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jv0 RCSB], [http://www.ebi.ac.uk/pdbsum/4jv0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jv0 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPO4_SULSO DPO4_SULSO]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113] | + | [https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[DNA polymerase|DNA polymerase]] | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed DNA polymerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Sulso]] | + | [[Category: Saccharolobus solfataricus P2]] |
| - | [[Category: Banerjee, S]] | + | [[Category: Banerjee S]] |
| - | [[Category: Shanmugam, G]] | + | [[Category: Shanmugam G]] |
| - | [[Category: Stone, M P]] | + | [[Category: Stone MP]] |
| - | [[Category: Dna adduct]]
| + | |
| - | [[Category: Dna polymerase]]
| + | |
| - | [[Category: Ternary complex of dpo4-dna-datp]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| Structural highlights
Function
DPO4_SACS2 Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
Publication Abstract from PubMed
Acrolein, a mutagenic aldehyde, reacts with deoxyguanosine (dG) to form 3-(2'-deoxy-beta-d-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-8-hydroxypyrimido[1 ,2-a] purin-10(3H)-one (gamma-OH-PdG). When placed opposite deoxycytosine (dC) in DNA, gamma-OH-PdG undergoes ring-opening to the N2-(3-oxopropyl)-dG. Ring-opening of the adduct has been hypothesized to facilitate nonmutagenic bypass, particularly by DNA polymerases of the Y family. This study examined the bypass of gamma-OH-PdG by Sulfolobus solfataricus Dpo4, the prototypic Y-family DNA polymerase, using templates that contained the adduct in either the 5'-CXG-3' or the 5'-TXG-3' sequence context. Although gamma-OH-PdG partially blocked Dpo4-catalyzed DNA synthesis, full primer extension was observed, and the majority of bypass products were error-free. Conversion of the adduct into an irreversibly ring-opened derivative prior to reaction facilitated bypass and further improved the fidelity. Structures of ternary Dpo4.DNA.dNTP complexes were determined with primers that either were positioned immediately upstream of the lesion (preinsertion complexes) or had a 3'-terminal dC opposite the lesion (postinsertion complexes); the incoming nucleotides, either dGTP or dATP, were complementary to the template 5'-neighbor nucleotide. In both postinsertion complexes, the adduct existed as ring-opened species, and the resulting base-pair featured Watson-Crick hydrogen bonding. The incoming nucleotide paired with the 5'-neighbor template, while the primer 3'-hydroxyl was positioned to facilitate extension. In contrast, gamma-OH-PdG was in the ring-closed form in both preinsertion complexes, and the overall structure did not favor catalysis. These data provide insights into gamma-OH-PdG chemistry during replication bypass by the Dpo4 DNA polymerase and may explain why gamma-OH-PdG-induced mutations due to primer-template misalignment are uncommon.
Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4.,Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP Chem Res Toxicol. 2013 Aug 16. PMID:23947567[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP. Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4. Chem Res Toxicol. 2013 Aug 16. PMID:23947567 doi:10.1021/tx400200b
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