4o5c: Difference between revisions
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==Structure of human DNA polymerase complexed with N7-MG as the template base in a 1-nucleotide gapped DNA== | ==Structure of human DNA polymerase complexed with N7-MG as the template base in a 1-nucleotide gapped DNA== | ||
<StructureSection load='4o5c' size='340' side='right' caption='[[4o5c]], [[Resolution|resolution]] 2.36Å' scene=''> | <StructureSection load='4o5c' size='340' side='right'caption='[[4o5c]], [[Resolution|resolution]] 2.36Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4o5c]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5C FirstGlance]. <br> | <table><tr><td colspan='2'>[[4o5c]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5C FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=FMG:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-7-METHYL-6-OXO-6,9-DIHYDRO-1H-PURIN-7-IUM'>FMG</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMG:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-7-METHYL-6-OXO-6,9-DIHYDRO-1H-PURIN-7-IUM'>FMG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3isb|3isb]], [[1bpx|1bpx]], [[4o5e|4o5e]], [[4o5k|4o5k]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3isb|3isb]], [[1bpx|1bpx]], [[4o5e|4o5e]], [[4o5k|4o5k]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4o5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5c OCA], [http://pdbe.org/4o5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o5c RCSB], [http://www.ebi.ac.uk/pdbsum/4o5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5c ProSAT]</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=4o5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5c OCA], [http://pdbe.org/4o5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o5c RCSB], [http://www.ebi.ac.uk/pdbsum/4o5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5c ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Human]] | |||
[[Category: Large Structures]] | |||
[[Category: Koag, M C]] | [[Category: Koag, M C]] | ||
[[Category: Lee, S]] | [[Category: Lee, S]] | ||
Revision as of 11:40, 10 April 2019
Structure of human DNA polymerase complexed with N7-MG as the template base in a 1-nucleotide gapped DNAStructure of human DNA polymerase complexed with N7-MG as the template base in a 1-nucleotide gapped DNA
Structural highlights
Function[DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.[1] [2] [3] [4] Publication Abstract from PubMedN7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilzation strategy. Specifically, we determined kinetic parameters for dCTP insertion opposite a chemically stable m7dG analogue, 2'-fluoro-m7dG (Fm7dG), by human DNA polymerase beta (polbeta) and solved three X-ray structures of polbeta in complex with the templating Fm7dG paired with incoming dCTP or dTTP analogues. The kinetic studies reveal that the templating Fm7dG slows polbeta catalysis approximately 300-fold, suggesting that m7dG in genomic DNA may impede replication by some DNA polymerases. The structural analysis reveals that Fm7dG forms a canonical Watson-Crick base pair with dCTP, but metal ion coordination is suboptimal for catalysis in the polbeta-Fm7dG:dCTP complex, which partially explains the slow insertion of dCTP opposite Fm7dG by polbeta. In addition, the polbeta-Fm7dG:dTTP structure shows open protein conformations and staggered base pair conformations, indicating that N7-methylation of dG does not promote a promutagenic replication. Overall, the first systematic studies on the effect of m7dG on DNA replication reveal that polbeta catalysis across m7dG is slow, yet highly accurate. Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine.,Koag MC, Kou Y, Ouzon-Shubeita H, Lee S Nucleic Acids Res. 2014 Jun 25. pii: gku554. PMID:24966350[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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