7PUT

Crystal structure of Thioredoxin Reductase from Brugia Malayi in complex with NADP(H)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biochemical and structural characterizations of thioredoxin reductase selenoproteins of the parasitic filarial nematodes Brugia malayi and Onchocerca volvulus.

Fata, F.Gencheva, R.Cheng, Q.Lullo, R.Ardini, M.Silvestri, I.Gabriele, F.Ippoliti, R.Bulman, C.A.Sakanari, J.A.Williams, D.L.Arner, E.S.J.Angelucci, F.

(2022) Redox Biol 51: 102278-102278

  • DOI: https://doi.org/10.1016/j.redox.2022.102278
  • Primary Citation of Related Structures:  
    7P0X, 7PUT, 7PVJ

  • PubMed Abstract: 

    Enzymes in the thiol redox systems of microbial pathogens are promising targets for drug development. In this study we characterized the thioredoxin reductase (TrxR) selenoproteins from Brugia malayi and Onchocerca volvulus, filarial nematode parasites and causative agents of lymphatic filariasis and onchocerciasis, respectively. The two filarial enzymes showed similar turnover numbers and affinities for different thioredoxin (Trx) proteins, but with a clear preference for the autologous Trx. Human TrxR1 (hTrxR1) had a high and similar specific activity versus the human and filarial Trxs, suggesting that, in vivo, hTrxR1 could possibly be the reducing agent of parasite Trxs once they are released into the host. Both filarial TrxRs were efficiently inhibited by auranofin and by a recently described inhibitor of human TrxR1 (TRi-1), but not as efficiently by the alternative compound TRi-2. The enzyme from B. malayi was structurally characterized also in complex with NADPH and auranofin, producing the first crystallographic structure of a nematode TrxR. The protein represents an unusual fusion of a mammalian-type TrxR protein architecture with an N-terminal glutaredoxin-like (Grx) domain lacking typical Grx motifs. Unlike thioredoxin glutathione reductases (TGRs) found in platyhelminths and mammals, which are also Grx-TrxR domain fusion proteins, the TrxRs from the filarial nematodes lacked glutathione disulfide reductase and Grx activities. The structural determinations revealed that the Grx domain of TrxR from B. malayi contains a cysteine (C22), conserved in TrxRs from clade IIIc nematodes, that directly interacts with the C-terminal cysteine-selenocysteine motif of the homo-dimeric subunit. Interestingly, despite this finding we found that altering C22 by mutation to serine did not affect enzyme catalysis. Thus, although the function of the Grx domain in these filarial TrxRs remains to be determined, the results obtained provide insights on key properties of this important family of selenoprotein flavoenzymes that are potential drug targets for treatment of filariasis.


  • Organizational Affiliation

    Dept. of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, 67100, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaredoxin domain-containing protein
A, B
598Brugia malayiMutation(s): 0 
Gene Names: bma-trxr-1Bma-trxr-1Bm2025BM_Bm2025
EC: 1.8.1.9
UniProt
Find proteins for A0A1I9G0T9 (Brugia malayi)
Explore A0A1I9G0T9 
Go to UniProtKB:  A0A1I9G0T9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I9G0T9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaredoxin domain-containing protein598Brugia malayiMutation(s): 0 
Gene Names: bma-trxr-1Bma-trxr-1Bm2025BM_Bm2025
EC: 1.8.1.9
UniProt
Find proteins for A0A1I9G0T9 (Brugia malayi)
Explore A0A1I9G0T9 
Go to UniProtKB:  A0A1I9G0T9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I9G0T9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
N [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
ATR (Subject of Investigation/LOI)
Query on ATR

Download Ideal Coordinates CCD File 
I [auth A]2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
YPTPYQSAVGGMFN-KQYNXXCUSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
2CO
Query on 2CO
A, B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.39α = 90
b = 260.287β = 90
c = 130.333γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary