6FBE

KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the third primer nucleotide.

• PDB DOI:  https://doi.org/10.2210/pdb6FBE/pdb
• NAKB: 6FBE

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermus aquaticus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-19 Released: 2018-09-26 
• Deposition Author(s): Kropp, H.M., Diederichs, K., Marx, A.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.203 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.

Kropp, H.M., Durr, S.L., Peter, C., Diederichs, K., Marx, A.

(2018) Proc Natl Acad Sci U S A 115: 9992-9997

• PubMed: 30224478 
• DOI: https://doi.org/10.1073/pnas.1811518115
• Primary Citation of Related Structures:  
  6FBC, 6FBD, 6FBE, 6FBF, 6FBG, 6FBH, 6FBI


• PubMed Abstract: 
  

DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification "moves" from the 3'-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme's activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.

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Organizational Affiliation: 

Konstanz Research School Chemical Biology, Universität Konstanz, 78464 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: 70.51 kDa 
• Atom Count: 5,376 
• Modelled Residue Count: 567 
• Deposited Residue Count: 569 
• 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	541	Thermus aquaticus	Mutation(s): 0  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 (5'-D(*GP*AP*CP*CP*AP*CP*GP*CP*AP*(OH3)P*CP*C)-3')	B	12	synthetic construct

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XG4	G [auth A]	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine C10 H17 N6 O12 P3 DWGAAFQEGIMTIA-KVQBGUIXSA-N
EDO	F [auth A], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.203 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.48	α = 90
b = 108.48	β = 90
c = 90.309	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Kropp, H.M., Diederichs, K., Marx, A.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2018-10-10
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2019-08-14
  Changes: Data collection, Structure summary