8P8O | pdb_00008p8o

M. tuberculosis dUTPase - Stl1-159 (StlNT) complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.286 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


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Literature

The homodimerization domain of the Stl repressor is crucial for efficient inhibition of mycobacterial dUTPase.

Toth, Z.S.Leveles, I.Nyiri, K.Nagy, G.N.Harmat, V.Jaroentomeechai, T.Ozohanics, O.Miller, R.L.Alvarez, M.B.Vertessy, B.G.Benedek, A.

(2024) Sci Rep 14: 27171-27171

  • DOI: https://doi.org/10.1038/s41598-024-76349-2
  • Primary Citation of Related Structures:  
    8CGA, 8P8O

  • PubMed Abstract: 

    The dUTPase is a key DNA repair enzyme in Mycobacterium tuberculosis, and it may serve as a novel promising anti-tuberculosis target. Stl repressor from Staphylococcus aureus was shown to bind to and inhibit dUTPases from various sources, and its expression in mycobacterial cells interfered with cell growth. To fine-tune and optimize Stl-induced inhibition of mycobacterial dUTPase, we aimed to decipher the molecular details of this interaction. Structural background of the complex between dUTPase and a truncated Stl lacking the repressor C-terminal homodimerization domain has been described, however, the effects of this truncation of Stl on enzyme binding and inhibition are still not known. Using several independent biophysical, structural and enzyme kinetic methods, here we show that lack of the repressor homodimerization domain strongly perturbs both enzyme binding and inhibition. We also investigated the role of a mycobacteria-specific loop in the Stl-interaction. Our results show that removal of this loop leads to a ten-fold increase in the apparent inhibition constant of Stl. We present a high-resolution three-dimensional structure of mycobacterial dUTPase lacking the genus-specific loop for structural insight. Our present data suggest that potent inhibition of mycobacterial dUTPase by Stl requires the wild-type full-length protein context.


  • Organizational Affiliation
    • Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary. toth.zoe@ttk.hu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase
A,
B,
C,
D,
E,
F [auth G]
174Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 3.6.1.23
UniProt
Find proteins for P9WNS5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNS5 
Go to UniProtKB:  P9WNS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNS5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Orf20165Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q9F0J8 (Staphylococcus aureus)
Explore Q9F0J8 
Go to UniProtKB:  Q9F0J8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F0J8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.286 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.669α = 90
b = 123.82β = 90
c = 170.229γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Development and Innovation Office (NKFIH)HungaryK119493

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release