5OMF image
Deposition Date 2017-07-31
Release Date 2017-12-20
Last Version Date 2024-11-13
Entry Detail
PDB ID:
5OMF
Keywords:
DNA BINDING PROTEIN
Title:
Closed, ternary structure of KOD DNA polymerase
Biological Source:
Source Organism:
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Taxon ID: 69014)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.09 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 2
5OMF validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase,DNA polymerase,DNA polymerase
Gene (Uniprot):pol
Chain IDs:A
Chain Length:774
Number of Molecules:1
Biological Source:Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
UniProt ID:P77933 Pfam ID:PF03104, PF00136 EC:2.7.7.7
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')
Chain IDs:C (auth: P)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
Chain IDs:B (auth: T)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
DTP
EDO
GOL
MG
MN
Primary Citation
Crystal structures of ternary complexes of archaeal B-family DNA polymerases.
PLoS ONE 12 e0188005 e0188005 (2017)
PMID: 29211756 DOI: 10.1371/journal.pone.0188005

Abstact

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.

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Primary Citation of related structures
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