4OOP

Arabidopsis thaliana dUTPase with with magnesium and alpha,beta-imido-dUTP

• PDB DOI: https://doi.org/10.2210/pdb4OOP/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-03 Released: 2015-04-08 
• Deposition Author(s): Inoguchi, N., Bajaj, M., Moriyama, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.209 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation.

Inoguchi, N., Chaiseeda, K., Yamanishi, M., Kim, M.K., Jang, Y., Bajaj, M., Chia, C.P., Becker, D.F., Moriyama, H.

(2015) BMC Res Notes 8: 784-784

• PubMed: 26666293 
• DOI: https://doi.org/10.1186/s13104-015-1760-1
• Primary Citation of Related Structures:  
  4OOP, 4OOQ


• PubMed Abstract: 
  

  Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) hydrolyzes dUTP to dUMP and pyrophosphate to maintain the cellular thymine-uracil ratio. dUTPase is also a target for cancer chemotherapy. However, the mechanism defining its substrate affinity remains unclear. Sequence comparisons of various dUTPases revealed that Arabidopsis thaliana dUTPase has a unique tryptophan at position 93, which potentially contributes to its degree of substrate affinity. To better understand the roles of tryptophan 93, A. thaliana dUTPase was studied.

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Organizational Affiliation: 

School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 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: 54.21 kDa 
• Atom Count: 3,658 
• Modelled Residue Count: 402 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A, B, C	166	Arabidopsis thaliana	Mutation(s): 0  Gene Names: DUT, DUT1, At3g46940, T6H20.30 EC: 3.6.1.23
UniProt
Find proteins for Q9STG6 (Arabidopsis thaliana) Explore Q9STG6  Go to UniProtKB:  Q9STG6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.209 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.089	α = 90
b = 70.68	β = 90
c = 75.064	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Inoguchi, N., Bajaj, M., Moriyama, H.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2016-07-06
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description