5OMF

Closed, ternary structure of KOD DNA polymerase

• PDB DOI: https://doi.org/10.2210/pdb5OMF/pdb
• NAKB: 5OMF

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermococcus kodakarensis KOD1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-07-31 Released: 2017-12-20 
• Deposition Author(s): Kropp, H.M., Betz, K., Wirth, J., Diederichs, K., Marx, A.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.234 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Crystal structures of ternary complexes of archaeal B-family DNA polymerases.

Kropp, H.M., Betz, K., Wirth, J., Diederichs, K., Marx, A.

(2017) PLoS One 12: e0188005-e0188005

• PubMed: 29211756 
• DOI: https://doi.org/10.1371/journal.pone.0188005
• Primary Citation of Related Structures:  
  5OMF, 5OMQ, 5OMV


• 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.

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Organizational Affiliation: 

Konstanz Research School Chemical Biology, University of Konstanz, Baden-Württemberg, Konstanz, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 101.01 kDa 
• Atom Count: 7,078 
• Modelled Residue Count: 782 
• Deposited Residue Count: 806 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase,DNA polymerase,DNA polymerase	A	774	Thermococcus kodakarensis KOD1	Mutation(s): 2  Gene Names: pol, TK0001 EC: 2.7.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P77933 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore P77933  Go to UniProtKB:  P77933

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')	B [auth T]	16	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')	C [auth P]	16	synthetic construct

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP (Subject of Investigation/LOI)	M [auth A]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
GOL	K [auth A], L [auth A], N [auth P]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.234 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.909	α = 90
b = 147.559	β = 90
c = 71.142	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Kropp, H.M., Betz, K., Wirth, J., Diederichs, K., Marx, A.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary