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

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P77933
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PCPTPGPTPGPGPCPCPGPTPGPGPTPC)-3')	B [auth T]	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPAPCPCPAPCPGPGPCPCPAPC)-3')	C [auth P]	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTP (Subject of Investigation/LOI) Query on DTP Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth P] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth P]	K [auth A], L [auth A], N [auth P]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth P] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth P]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History (Full details and data files)

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