8QKY | pdb_00008qky

Bacteriophage T5 dUTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.211 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history

Literature

Bacteriophage T5 dUTPase: Combination of Common Enzymatic and Novel Functions.

Glukhov, A.Marchenkov, V.Dzhus, U.Krutilina, A.Selikhanov, G.Gabdulkhakov, A.

(2024) Int J Mol Sci 25

  • DOI: https://doi.org/10.3390/ijms25020892
  • Primary Citation Related Structures: 
    8QKY, 8QLD

  • PubMed Abstract: 

    The main function of dUTPases is to regulate the cellular levels of dUTP and dTTP, thereby playing a crucial role in DNA repair mechanisms. Despite the fact that mutant organisms with obliterated dUTPase enzymatic activity remain viable, it is not possible to completely knock out the dut gene due to the lethal consequences of such a mutation for the organism. As a result, it is considered that this class of enzymes performs an additional function that is essential for the organism's survival. In this study, we provide evidence that the dUTPase of bacteriophage T5 fulfills a supplemental function, in addition to its canonical role. We determined the crystal structure of bacteriophage T5 dUTPase with a resolution of 2.0 Å, and we discovered a distinct short loop consisting of six amino acid residues, representing a unique structural feature specific to the T5-like phages dUTPases. The removal of this element did not affect the overall structure of the homotrimer, but it had significant effects on the development of the phage. Furthermore, it was shown that the enzymatic function and the novel function of the bacteriophage T5 dUTPase are unrelated and independent from each other.


  • Organizational Affiliation
    • Institute of Protein Research RAS, 142290 Pushchino, Russia.

Macromolecule Content 

  • Total Structure Weight: 48.76 kDa 
  • Atom Count: 3,378 
  • Modeled Residue Count: 409 
  • Deposited Residue Count: 444 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase
A, B, C
148Escherichia phage T5Mutation(s): 0 
Gene Names: DUT
EC: 3.6.1.23
UniProt
Find proteins for O48500 (Escherichia phage T5)
Explore O48500 
Go to UniProtKB:  O48500
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO48500
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.211 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.43α = 90
b = 78.43β = 90
c = 86.94γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation23-24-00510

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references