SASDE54: Tryparedoxin W39A, in the presence of inhibitor CFT (2-(chloromet...

Basic information

• Entry: Database: SASBDB / ID: SASDE54

Sample

Tryparedoxin W39A, in the presence of inhibitor CFT (2-(chloromethyl)-5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one)

• Tryparedoxin W39A (protein), Trypanosoma brucei brucei

Function / homology

Function:

thioredoxin-disulfide reductase (NADPH) activity

Domain/homology:

TryX and NRX, thioredoxin domain / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily

Component:

Tryparedoxin

• Biological species: Trypanosoma brucei brucei (eukaryote)
• Citation: Journal: Angew Chem Int Ed Engl / Year: 2019; Title: Inhibitor-Induced Dimerization of an Essential Oxidoreductase from African Trypanosomes.; Authors: Annika Wagner / Thien Anh Le / Martha Brennich / Philipp Klein / Nicole Bader / Erika Diehl / Daniel Paszek / A Katharina Weickhmann / Natalie Dirdjaja / R Luise Krauth-Siegel / Bernd Engels / Till Opatz / Hermann Schindelin / Ute A Hellmich / ; Abstract: Trypanosomal and leishmanial infections claim tens of thousands of lives each year. The metabolism of these unicellular eukaryotic parasites differs from the human host and their enzymes thus constitute promising drug targets. Tryparedoxin (Tpx) from Trypanosoma brucei is the essential oxidoreductase in the parasite's hydroperoxide-clearance cascade. In vitro and in vivo functional assays show that a small, selective inhibitor efficiently inhibits Tpx. With X-ray crystallography, SAXS, analytical SEC, SEC-MALS, MD simulations, ITC, and NMR spectroscopy, we show how covalent binding of this monofunctional inhibitor leads to Tpx dimerization. Intra- and intermolecular inhibitor-inhibitor, protein-protein, and inhibitor-protein interactions stabilize the dimer. The behavior of this efficient antitrypanosomal molecule thus constitutes an exquisite example of chemically induced dimerization with a small, monovalent ligand that can be exploited for future drug design.

Contact author

• Martha Brennich (EMBL, European Molecular Biology Laboratory (EMBL) - Grenoble Outstation, Grenoble, France)

Models

• Model #2338: ; Type: atomic / Chi-square value: 1.87 / P-value: 0.000002; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2339: ; Type: atomic / Chi-square value: 1.87 / P-value: 0.000002; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Tryparedoxin W39A, in the presence of inhibitor CFT (2-(chloromethyl)-5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one)
• Buffer: Name: 10 mM HEPES pH 7.5, 50 mM NaCl / pH: 7.5

Entity #1271

Type: protein / Description: Tryparedoxin W39A / Formula weight: 15.702 / Source: Trypanosoma brucei brucei / References: UniProt: O77404
Sequence:

GSGLAKYLPG ATNLLSKSGE VSLGSLVGKT VFLYFSASAC PPCRGFTPVL AEFYEKHHVA KNFEVVLISW DENESDFHDY YGKMPWLALP FDQRSTVSEL GKTFGVESIP TLITINADTG AIIGTQARTR VIEDPDGANF PWPN

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.869 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Tryparedoxin W39A, in the presence of CFT / Measurement date: May 31, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Unit: 1/nm /

	Min	Max
Q	0.0373	4.9279

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 922 /

	Min	Max
Q	0.168674	4.49139
P(R) point	1	922
R	0	5.83

Result

Type of curve: sec
Comments: SEC column type: GE Healthcare S75 3.2/300; Sample Injection Concentration = 10 mg/mL; Column flow-rate = 0.1 mL/min.

	Experimental	Porod
MW	15 kDa	15 kDa
Volume	-	26.07 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	8.247	8.25	0.01
Radius of gyration, Rg	1.6 nm	1.6 nm	0.01

	Min	Max
D	-	5.83
Guinier point	29	165