6BPY | pdb_00006bpy

Aspergillus fumigatus Thioredoxin Reductase

PDB DOI: https://doi.org/10.2210/pdb6BPY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus fumigatus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-27 Released: 2019-01-09
Deposition Author(s): Marshall, A.C., Bruning, J.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.261 (Depositor), 0.281 (DCC)
R-Value Work:
0.231 (Depositor), 0.265 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure, Mechanism, and Inhibition ofAspergillus fumigatusThioredoxin Reductase.

Marshall, A.C., Kidd, S.E., Lamont-Friedrich, S.J., Arentz, G., Hoffmann, P., Coad, B.R., Bruning, J.B.

(2019) Antimicrob Agents Chemother 63

PubMed: 30642940 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/AAC.02281-18
Primary Citation Related Structures:
6BPY

PubMed Abstract:
Aspergillus fumigatus infections are associated with high mortality rates and high treatment costs. Limited available antifungals and increasing antifungal resistance highlight an urgent need for new antifungals. Thioredoxin reductase (TrxR) is essential for maintaining redox homeostasis and presents as a promising target for novel antifungals. We show that ebselen [2-phenyl-1,2-benzoselenazol-3(2H)-one] is an inhibitor of A. fumigatus TrxR ( K _i = 0.22 μM) and inhibits growth of Aspergillus spp., with in vitro MIC values of 16 to 64 µg/ml. Mass spectrometry analysis demonstrates that ebselen interacts covalently with a catalytic cysteine of TrxR, Cys148. We also present the X-ray crystal structure of A. fumigatus TrxR and use in silico modeling of the enzyme-inhibitor complex to outline key molecular interactions. This provides a scaffold for future design of potent and selective antifungal drugs that target TrxR, improving the potency of ebselen toward inhbition of A. fumigatus growth.

Organizational Affiliation

Institute for Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.

Macromolecule Content

Total Structure Weight: 83.92 kDa
Atom Count: 5,003
Modeled Residue Count: 643
Deposited Residue Count: 748
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A, B	374	Aspergillus fumigatus	Mutation(s): 0 Gene Names: CDV57_04819, CDV58_04527 EC: 1.8.1.9
UniProt
Find proteins for A0A229Y1X4 (Aspergillus fumigatus) Explore A0A229Y1X4 Go to UniProtKB: A0A229Y1X4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A229Y1X4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A], K [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain I [auth A] mmCIF format, chain S [auth B] mmCIF format, chain I [auth A]	I [auth A], S [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain S [auth B] Interactions & Density Focus chain I [auth A] Focus chain S [auth B]
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], L [auth B], M [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] N [auth B] O [auth B] P [auth B] G [auth A], H [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.261 (Depositor), 0.281 (DCC)
R-Value Work: 0.231 (Depositor), 0.265 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.22	α = 90
b = 159.22	β = 90
c = 121.37	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-01-09

Deposition Author(s):

Marshall, A.C.

Bruning, J.B.

Revision History (Full details and data files)

Version 1.0: 2019-01-09
Type: Initial release
Version 1.1: 2019-09-04
Changes: Data collection, Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary