8CGA | pdb_00008cga

Structure of Mycobacterium tuberculosis dUTPase delta 133A-137S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

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


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 nucleotidohydrolase169Mycobacterium tuberculosisMutation(s): 0 
Gene Names: dutRv2697cMTCY05A6.18c
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
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUP (Subject of Investigation/LOI)
Query on DUP

Download Ideal Coordinates CCD File 
B [auth A]2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
F [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.249α = 90
b = 55.249β = 90
c = 83.751γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Development and Innovation Office (NKFIH)HungaryK119493
National Research Development and Innovation Office (NKFIH)HungaryK135231
National Research Development and Innovation Office (NKFIH)HungaryVEKOP-2.3.2-16-2017-00013
National Research Development and Innovation Office (NKFIH)HungaryNKP-2018-1.2.1-NKP-2018-00005
National Research Development and Innovation Office (NKFIH)HungaryTKP2021-EGA-02

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references, Structure summary