Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 364.77 kDa 
• Atom Count: 24,538 
• Modelled Residue Count: 2,980 
• Deposited Residue Count: 3,030 
• Unique protein chains: 1

 4XDS

Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia coli with Nickel

• PDB DOI:  https://doi.org/10.2210/pdb4XDS/pdb

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-19 Released: 2015-02-25 
• Deposition Author(s): Singh, D., Gawel, D., Itsko, M., Krahn, J.M., London, R.E., Schaaper, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.209 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Structure of Escherichia coli dGTP Triphosphohydrolase: A HEXAMERIC ENZYME WITH DNA EFFECTOR MOLECULES.

Singh, D., Gawel, D., Itsko, M., Hochkoeppler, A., Krahn, J.M., London, R.E., Schaaper, R.M.

(2015) J Biol Chem 290: 10418-10429

• PubMed: 25694425 
• DOI: https://doi.org/10.1074/jbc.M115.636936
• Primary Citation of Related Structures:  
  4X9E, 4XDS


• PubMed Abstract: 
  

The Escherichia coli dgt gene encodes a dGTP triphosphohydrolase whose detailed role still remains to be determined. Deletion of dgt creates a mutator phenotype, indicating that the dGTPase has a fidelity role, possibly by affecting the cellular dNTP pool. In the present study, we have investigated the structure of the Dgt protein at 3.1-Å resolution. One of the obtained structures revealed a protein hexamer that contained two molecules of single-stranded DNA. The presence of DNA caused significant conformational changes in the enzyme, including in the catalytic site of the enzyme. Dgt preparations lacking DNA were able to bind single-stranded DNA with high affinity (Kd ∼ 50 nM). DNA binding positively affected the activity of the enzyme: dGTPase activity displayed sigmoidal (cooperative) behavior without DNA but hyperbolic (Michaelis-Menten) kinetics in its presence, consistent with a specific lowering of the apparent Km for dGTP. A mutant Dgt enzyme was also created containing residue changes in the DNA binding cleft. This mutant enzyme, whereas still active, was incapable of DNA binding and could no longer be stimulated by addition of DNA. We also created an E. coli strain containing the mutant dgt gene on the chromosome replacing the wild-type gene. The mutant also displayed a mutator phenotype. Our results provide insight into the allosteric regulation of the enzyme and support a physiologically important role of DNA binding.

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Organizational Affiliation: 

From the Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyguanosinetriphosphate triphosphohydrolase	A, B, C, D, E, F	505	Escherichia coli K-12	Mutation(s): 0  Gene Names: dgt, b0160, JW0156 EC: 3.1.5.1
UniProt
Find proteins for P15723 (Escherichia coli (strain K12)) Explore P15723  Go to UniProtKB:  P15723

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AB [auth D], AC [auth F], BA [auth C], BB [auth D], BC [auth F], CA [auth C], CB [auth D], CC [auth F], DA [auth C], DC [auth F], EA [auth C], EB [auth E], EC [auth F], FA [auth C], FB [auth E], FC [auth F], GA [auth C], GB [auth E], GC [auth F], H [auth A], HA [auth C], HB [auth E], HC [auth F], I [auth A], IA [auth C], IB [auth E], IC [auth F], J [auth A], JA [auth C], JB [auth E], JC [auth F], K [auth A], KA [auth C], KB [auth E], KC [auth F], L [auth A], LA [auth C], LB [auth E], LC [auth F], M [auth A], MA [auth C], MB [auth E], MC [auth F], N [auth A], NA [auth C], NB [auth E], O [auth A], OA [auth C], OB [auth E], P [auth A], PA [auth D], PB [auth E], Q [auth A], QB [auth E], RA [auth D], RB [auth E], S [auth B], SA [auth D], SB [auth E], T [auth B], TA [auth D], TB [auth F], U [auth B], UA [auth D], V [auth B], VA [auth D], VB [auth F], W [auth B], WA [auth D], WB [auth F], X [auth B], XA [auth D], XB [auth F], Y [auth B], YA [auth D], YB [auth F], Z [auth B], ZA [auth D], ZB [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	AA [auth C], DB [auth E], G [auth A], QA [auth D], R [auth B], UB [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.209 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.8	α = 90
b = 189.8	β = 90
c = 296.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Singh, D., Gawel, D., Itsko, M., Krahn, J.M., London, R.E., Schaaper, R.M.

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2015-04-29
  Changes: Database references