5OXJ | pdb_00005oxj

Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair

• PDB DOI: https://doi.org/10.2210/pdb5OXJ/pdb
• NAKB: 5OXJ

• Classification: TRANSFERASE
• Organism(s): Thermus aquaticus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-09-06 Released: 2017-11-29 
• Deposition Author(s): Betz, K., Diederichs, K., Marx, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase.

Betz, K., Nilforoushan, A., Wyss, L.A., Diederichs, K., Sturla, S.J., Marx, A.

(2017) Chem Commun (Camb) 53: 12704-12707

• PubMed: 29136072 
• DOI: https://doi.org/10.1039/c7cc07173f
• Primary Citation Related Structures: 
  5O7T, 5OXJ


• PubMed Abstract: 
  

  The possibility to sequence cytotoxic O ⁶ -alkylG DNA adducts would greatly benefit research. Recently we reported a benzimidazole-derived nucleotide that is selectively incorporated opposite the damaged site by a mutated DNA polymerase. Here we provide the structural basis for this reaction which may spur future developments in DNA damage sequencing.

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Organizational Affiliation: 
• Department of Chemistry & Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.36 kDa 
• Atom Count: 4,946 
• Modeled Residue Count: 560 
• Deposited Residue Count: 568 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I, thermostable	A	540	Thermus aquaticus	Mutation(s): 1  Gene Names: polA, pol1 EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus) Explore P19821  Go to UniProtKB:  P19821

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA primer	B	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA template	C	16	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NZI	F [auth A]	[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate C12 H17 N2 O13 P3 OMCWLYQAPHJDBD-HBNTYKKESA-N
ACT	G [auth A], H [auth A], K [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	I [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.347	α = 90
b = 109.347	β = 90
c = 90.636	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Betz, K., Diederichs, K., Marx, A.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description