7om3: Difference between revisions
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==== | ==Crystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine containing template== | ||
<StructureSection load='7om3' size='340' side='right'caption='[[7om3]]' scene=''> | <StructureSection load='7om3' size='340' side='right'caption='[[7om3]], [[Resolution|resolution]] 1.92Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[7om3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1] 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=7OM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OM3 FirstGlance]. <br> | ||
</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=7om3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7om3 OCA], [https://pdbe.org/7om3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7om3 RCSB], [https://www.ebi.ac.uk/pdbsum/7om3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7om3 ProSAT]</span></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]] 1.92Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7om3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7om3 OCA], [https://pdbe.org/7om3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7om3 RCSB], [https://www.ebi.ac.uk/pdbsum/7om3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7om3 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/DPOL_THEKO DPOL_THEKO] Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the "homing site" in gene that lack the intein. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5'-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases. | |||
Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase.,Kropp HM, Ludmann S, Diederichs K, Betz K, Marx A Chembiochem. 2021 Nov 3;22(21):3060-3066. doi: 10.1002/cbic.202100306. Epub 2021 , Sep 14. PMID:34486208<ref>PMID:34486208</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7om3" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: Thermococcus kodakarensis KOD1]] | |||
[[Category: Betz K]] | |||
[[Category: Diederichs K]] | |||
[[Category: Kropp HM]] | |||
[[Category: Marx A]] | |||
Latest revision as of 15:52, 1 February 2024
Crystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine containing templateCrystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine containing template
Structural highlights
FunctionDPOL_THEKO Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the "homing site" in gene that lack the intein. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'. Publication Abstract from PubMedWith increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5'-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases. Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase.,Kropp HM, Ludmann S, Diederichs K, Betz K, Marx A Chembiochem. 2021 Nov 3;22(21):3060-3066. doi: 10.1002/cbic.202100306. Epub 2021 , Sep 14. PMID:34486208[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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