6ph6: Difference between revisions
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==Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream== | |||
<StructureSection load='6ph6' size='340' side='right'caption='[[6ph6]], [[Resolution|resolution]] 2.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ph6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PH6 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ph6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ph6 OCA], [https://pdbe.org/6ph6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ph6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ph6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ph6 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DPOLB_HUMAN 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.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
DNA polymerase beta has two DNA-binding domains that interact with the opposite sides of short DNA gaps. These domains contribute two activities that modify the 5'- and 3'-margins of gapped DNA during base excision repair. DNA gaps greater than one-nucleotide pose an architectural and logistical problem for the two domains to interact with their respective DNA termini. Here, crystallographic and kinetic analyses of two-nucleotide gap-filling DNA synthesis revealed that the fidelity of DNA synthesis depends on local sequence context. This was due to template dynamics that altered which of the two template nucleotides in the gap served as the coding nucleotide. We observed that when a purine nucleotide is in the first coding position, DNA synthesis fidelity is similar to that observed with a one-nucleotide gap. However, when the initial templating nucleotide is a pyrimidine, fidelity was decreased. If the first templating nucleotide was cytidine, there was a significantly higher probability that the downstream template nucleotide coded for the incoming nucleotide. This dNTP-stabilized misalignment reduced base-substitution and frameshift-deletion fidelities. A crystal structure of a binary DNA product complex revealed that the cytidine in the first templating site is in an extra-helical position, permitting the downstream template nucleotide to occupy the coding position. These results indicate that DNA polymerase beta can induce a strain in the DNA that modulates the position of the coding nucleotide and thereby impacts the identity of the incoming nucleotide. Our findings demonstrate that "correct" DNA synthesis can result in errors when template dynamics induce coding ambiguity. | |||
DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context.,Howard MJ, Cavanaugh NA, Batra VK, Shock DD, Beard WA, Wilson SH J Biol Chem. 2019 Dec 4. pii: RA119.010594. doi: 10.1074/jbc.RA119.010594. PMID:31801827<ref>PMID:31801827</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6ph6" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
==See Also== | |||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | |||
[[Category: Batra VK]] | |||
[[Category: Wilson SH]] | |||
Latest revision as of 10:29, 11 October 2023
Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstreamTernary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream
Structural highlights
FunctionDPOLB_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 PubMedDNA polymerase beta has two DNA-binding domains that interact with the opposite sides of short DNA gaps. These domains contribute two activities that modify the 5'- and 3'-margins of gapped DNA during base excision repair. DNA gaps greater than one-nucleotide pose an architectural and logistical problem for the two domains to interact with their respective DNA termini. Here, crystallographic and kinetic analyses of two-nucleotide gap-filling DNA synthesis revealed that the fidelity of DNA synthesis depends on local sequence context. This was due to template dynamics that altered which of the two template nucleotides in the gap served as the coding nucleotide. We observed that when a purine nucleotide is in the first coding position, DNA synthesis fidelity is similar to that observed with a one-nucleotide gap. However, when the initial templating nucleotide is a pyrimidine, fidelity was decreased. If the first templating nucleotide was cytidine, there was a significantly higher probability that the downstream template nucleotide coded for the incoming nucleotide. This dNTP-stabilized misalignment reduced base-substitution and frameshift-deletion fidelities. A crystal structure of a binary DNA product complex revealed that the cytidine in the first templating site is in an extra-helical position, permitting the downstream template nucleotide to occupy the coding position. These results indicate that DNA polymerase beta can induce a strain in the DNA that modulates the position of the coding nucleotide and thereby impacts the identity of the incoming nucleotide. Our findings demonstrate that "correct" DNA synthesis can result in errors when template dynamics induce coding ambiguity. DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context.,Howard MJ, Cavanaugh NA, Batra VK, Shock DD, Beard WA, Wilson SH J Biol Chem. 2019 Dec 4. pii: RA119.010594. doi: 10.1074/jbc.RA119.010594. PMID:31801827[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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