7omb

Crystal structure of KOD DNA Polymerase in a ternary complex with a p/t duplex containing an extended 5' single stranded template overhang

spinqualitylabelsall models 7omb, resolution 2.01Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7omb is a 3 chain structure with sequence from Thermococcus kodakarensis KOD1 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.01Å Ligands: DOC, DTP, EDO, MG, MN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function 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'. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also DNA polymerase 3D structures

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