4jv0: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==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=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4jv0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus 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 [http://oca.weizmann.ac.il/oca-docs/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> | |||
<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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4juz|4juz]], [[4jv1|4jv1]], [[4jv2|4jv2]]</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 Sulfolobus solfataricus P2])</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://www.rcsb.org/pdb/explore.do?structureId=4jv0 RCSB], [http://www.ebi.ac.uk/pdbsum/4jv0 PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:23947567</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== | ==See Also== | ||
*[[DNA polymerase|DNA polymerase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Sulfolobus solfataricus p2]] | [[Category: Sulfolobus solfataricus p2]] | ||
[[Category: Banerjee, S | [[Category: Banerjee, S]] | ||
[[Category: Shanmugam, G | [[Category: Shanmugam, G]] | ||
[[Category: Stone, M P | [[Category: Stone, M P]] | ||
[[Category: Dna adduct]] | [[Category: Dna adduct]] | ||
[[Category: Dna polymerase]] | [[Category: Dna polymerase]] | ||
[[Category: Ternary complex of dpo4-dna-datp]] | [[Category: Ternary complex of dpo4-dna-datp]] | ||
[[Category: Transferase-dna complex]] | [[Category: Transferase-dna complex]] | ||
Revision as of 18:25, 21 December 2014
Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4
Structural highlights
Publication Abstract from PubMedAcrolein, 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 AlsoReferences
|
| ||||||||||||||||||||||||