3SYZ

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase

• PDB DOI: https://doi.org/10.2210/pdb3SYZ/pdb
• NAKB: 3SYZ

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


• Deposited: 2011-07-18 Released: 2012-06-06 
• Deposition Author(s): Betz, K., Diederichs, K., Marx, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.201 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Starting Model: experimental

Literature

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Dwyer, T.J., Ordoukhanian, P., Romesberg, F.E., Marx, A.

(2012) Nat Chem Biol 8: 612-614

• PubMed: 22660438 
• DOI: https://doi.org/10.1038/nchembio.966
• Primary Citation of Related Structures:  
  3RTV, 3SV3, 3SV4, 3SYZ, 3SZ2


• PubMed Abstract: 
  

  Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

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Organizational Affiliation: 

Department of Chemistry, Universität Konstanz, 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: 70.77 kDa 
• Atom Count: 5,305 
• Modelled Residue Count: 568 
• 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: pol I, pol1, polA 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
(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(*AP*AP*AP*(BMN)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')	C	16	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], N [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	O [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.201 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.529	α = 90
b = 108.529	β = 90
c = 90.524	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: 2012-06-06 
Deposition Author(s): Betz, K., Diederichs, K., Marx, A.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-07-04
  Changes: Database references
• Version 1.2: 2012-09-12
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description