5OMF

Closed, ternary structure of KOD DNA polymerase

Summary for 5OMF

• Entry DOI: 10.2210/pdb5omf/pdb
• Descriptor: DNA polymerase,DNA polymerase,DNA polymerase, DNA (5'-D(P*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3'), ... (9 entities in total)
• Functional Keywords: dna replication dna polymerase archaea, dna binding protein
• Biological source: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1); More
• Total number of polymer chains: 3
• Total formula weight: 101008.74

Authors

Kropp, H.M.,Betz, K.,Wirth, J.,Diederichs, K.,Marx, A. (deposition date: 2017-07-31, release date: 2017-12-20, Last modification date: 2024-11-13)

Primary citation

Kropp, H.M.,Betz, K.,Wirth, J.,Diederichs, K.,Marx, A.
Crystal structures of ternary complexes of archaeal B-family DNA polymerases.
PLoS ONE, 12:e0188005-e0188005, 2017

PubMed Abstract: Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.

PubMed: 29211756
DOI: 10.1371/journal.pone.0188005

Experimental method

X-RAY DIFFRACTION (2.092 Å)