4DFP

Crystal structure of the large fragment of DNA Polymerase I from Thermus aqauticus in a ternary complex with 7-(aminopentinyl)-7-deaza-dGTP

• PDB DOI: https://doi.org/10.2210/pdb4DFP/pdb
• NAKB: 4DFP

• Classification: TRANSFERASE/DNA
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-24 Released: 2012-05-16 
• Deposition Author(s): Bergen, K., Steck, A., Struett, S., Baccaro, A., Welte, W., Diederichs, K., Marx, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.

Bergen, K., Steck, A.L., Strutt, S., Baccaro, A., Welte, W., Diederichs, K., Marx, A.

(2012) J Am Chem Soc 134: 11840-11843

• PubMed: 22475415 
• DOI: https://doi.org/10.1021/ja3017889


• PubMed Abstract: 
  

  The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.

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Organizational Affiliation: 

Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 70.82 kDa 
• Atom Count: 5,219 
• Modelled Residue Count: 567 
• 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): 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*GP*CP*GP*CP*(DOC))-3')	B	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-d(AAACGGCGCCGTGGTC)-3'	C	16	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0L7	K [auth A]	2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one C16 H24 N5 O13 P3 XIWGGMXHUSVMFH-QJPTWQEYSA-N
EDO	F [auth A], H [auth A], L [auth A], N [auth A], T [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	G [auth A], I [auth A], J [auth A], O [auth A], Q [auth B], S [auth C], U [auth C]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	D [auth A], E [auth A], M [auth A], P [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.448	α = 90
b = 108.448	β = 90
c = 90.435	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Bergen, K., Steck, A., Struett, S., Baccaro, A., Welte, W., Diederichs, K., Marx, A.

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2012-08-08
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description