5F9K

Dictyostelium discoideum dUTPase at 2.2 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb5F9K/pdb

• Classification: HYDROLASE
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-09 Released: 2016-12-14 
• Deposition Author(s): Inoguchi, N., Chia, C.P., Heck, K., Moriyama, H.
• Funding Organization(s): The John C. and Nettie V. David Memorial Trust Fund of the University of Nebraska Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.251 
• R-Value Work: 0.209 
• R-Value Observed: 0.213 

Literature

Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by its N-terminus.

Chia, C.P., Inoguchi, N., Varon, K.C., Bartholomai, B.M., Moriyama, H.

(2020) BMC Res Notes 13: 16-16

• PubMed: 31910901 
• DOI: https://doi.org/10.1186/s13104-019-4879-7
• Primary Citation of Related Structures:  
  5F9K


• PubMed Abstract: 
  

  The nuclear and mitochondrial genomes of Dictyostelium discoideum, a unicellular eukaryote, have relatively high A+T-contents of 77.5% and 72.65%, respectively. To begin to investigate how the pyrimidine biosynthetic pathway fulfills the demand for dTTP, we determined the catalytic properties and structure of the key enzyme deoxyuridine triphosphate nucleotidohydrolase (dUTPase) that hydrolyzes dUTP to dUMP, the precursor of dTTP.

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Organizational Affiliation: 

School of Biological Sciences, Univ. Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 48.24 kDa 
• Atom Count: 3,181 
• Modelled Residue Count: 386 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A, B, C	146	Dictyostelium discoideum	Mutation(s): 0  Gene Names: dut, DDB_G0293374 EC: 3.6.1.23
UniProt
Find proteins for Q54BW5 (Dictyostelium discoideum) Explore Q54BW5  Go to UniProtKB:  Q54BW5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUP	D [auth A], E [auth B], L [auth C]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N
SO4	K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	F [auth B], G [auth B], H [auth B], I [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.251 
• R-Value Work: 0.209 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.633	α = 90
b = 72.458	β = 90
c = 75.158	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Inoguchi, N., Chia, C.P., Heck, K., Moriyama, H.

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Funding Organization	Location	Grant Number
The John C. and Nettie V. David Memorial Trust Fund of the University of Nebraska Foundation	United States	--

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2020-01-22
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description