6RTM

Thioredoxin glutathione reductase from Schistosoma mansoni in complex with 1-[(dimethylamino)methyl]-2-naphthol at 2 hour of soaking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ectopic suicide inhibition of thioredoxin glutathione reductase.

Silvestri, I.Lyu, H.Fata, F.Banta, P.R.Mattei, B.Ippoliti, R.Bellelli, A.Pitari, G.Ardini, M.Petukhova, V.Thatcher, G.R.J.Petukhov, P.A.Williams, D.L.Angelucci, F.

(2019) Free Radic. Biol. Med. 147: 200-211

  • DOI: 10.1016/j.freeradbiomed.2019.12.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Selective suicide inhibitors represent a seductively attractive approach for inactivation of therapeutically relevant enzymes since they are generally devoid of off-target toxicity in vivo. While most suicide inhibitors are converted to reactive spec ...

    Selective suicide inhibitors represent a seductively attractive approach for inactivation of therapeutically relevant enzymes since they are generally devoid of off-target toxicity in vivo. While most suicide inhibitors are converted to reactive species at enzyme active sites, theoretically bioactivation can also occur in ectopic (secondary) sites that have no known function. Here, we report an example of such an "ectopic suicide inhibition", an unprecedented bioactivation mechanism of a suicide inhibitor carried out by a non-catalytic site of thioredoxin glutathione reductase (TGR). TGR is a promising drug target to treat schistosomiasis, a devastating human parasitic disease. Utilizing hits selected from a high throughput screening campaign, time-resolved X-ray crystallography, molecular dynamics, mass spectrometry, molecular modeling, protein mutagenesis and functional studies, we find that 2-naphtholmethylamino derivatives bound to this novel ectopic site of Schistosoma mansoni (Sm)TGR are transformed to covalent modifiers and react with its mobile selenocysteine-containing C-terminal arm. In particular, one 2-naphtholmethylamino compound is able to specifically induce the pro-oxidant activity in the inhibited enzyme. Since some 2-naphtholmethylamino analogues show worm killing activity and the ectopic site is not conserved in human orthologues, a general approach to development of novel and selective anti-parasitic therapeutics against schistosoma is proposed.


    Organizational Affiliation

    Dept. of Biochemical Sciences, Sapienza University of Rome, Italy.,Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA.,Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy. Electronic address: francesco.angelucci@univaq.it.,Dept. of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.,Dept. of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA. Electronic address: pap4@uic.edu.,Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA. Electronic address: david_williams@rush.edu.,Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thioredoxin glutathione reductase
A
598Schistosoma mansoniMutation(s): 0 
EC: 1.8.1.9
Find proteins for G4V8J4 (Schistosoma mansoni)
Go to UniProtKB:  G4V8J4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
KJH
Query on KJH

Download SDF File 
Download CCD File 
A
1-methylidenenaphthalen-2-one
C11 H8 O
CPUOMPRQOCEZSL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.042α = 90.00
b = 102.002β = 112.78
c = 58.540γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR33AI127635

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-15
    Type: Database references