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- PDB-6bu7: Crystal structure of Trypanothione Reductase from Trypanosoma bru... -

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Basic information

Entry
Database: PDB / ID: 6bu7
TitleCrystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor RD130 1-[2-(Piperidin-4-yl)ethyl]-5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole
ComponentsTrypanothione reductase
KeywordsOxidoreductase/Inhibitor / Trypanosoma / Inhibitor / Complex / Sleeping Sickness / Oxidoreductase-Inhibitor complex
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress ...trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / nucleoplasm / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-RD0 / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsBryson, S. / De Gasparo, R. / Krauth-Siegel, R.L. / Diederich, F. / Pai, E.F.
Funding support Canada, Switzerland, Germany, 4items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-04877 Canada
Canada Research Chairs Canada
ETH Research CouncilETH-01 13-2 Switzerland
German Research Foundation (DFG)KR-1242/8-1 Germany
Citation
Journal: ChemMedChem / Year: 2018
Title: Biological Evaluation and X-ray Co-crystal Structures of Cyclohexylpyrrolidine Ligands for Trypanothione Reductase, an Enzyme from the Redox Metabolism of Trypanosoma.
Authors: De Gasparo, R. / Brodbeck-Persch, E. / Bryson, S. / Hentzen, N.B. / Kaiser, M. / Pai, E.F. / Krauth-Siegel, R.L. / Diederich, F.
#1: Journal: ChemMedChem / Year: 2014
Title: Binding to large enzyme pockets: small-molecule inhibitors of trypanothione reductase.
Authors: Persch, E. / Bryson, S. / Todoroff, N.K. / Eberle, C. / Thelemann, J. / Dirdjaja, N. / Kaiser, M. / Weber, M. / Derbani, H. / Brun, R. / Schneider, G. / Pai, E.F. / Krauth-Siegel, R.L. / Diederich, F.
History
DepositionDec 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypanothione reductase
B: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,81817
Polymers106,9962
Non-polymers3,82215
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The dimeric nature has also been well established by ultracentrifugation, crystallography and in-crystal chemistry.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11670 Å2
ΔGint-121 kcal/mol
Surface area39100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.283, 117.283, 224.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Trypanothione reductase


Mass: 53497.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb10.406.0520 / Plasmid: pET3aTbTryR
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q389T8, trypanothione-disulfide reductase

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Non-polymers , 6 types, 34 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-RD0 / 1-[2-(piperidin-4-yl)ethyl]-5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole


Mass: 462.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H38N4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Adding 5 microL of 10 mM inhibitor in DMSO to 95 microL of protein solution (10mg/ml; 20 mM TRIS, pH8.0), then mixing 2 microL of protein solution with 2 microL of well solution (0.1 M ...Details: Adding 5 microL of 10 mM inhibitor in DMSO to 95 microL of protein solution (10mg/ml; 20 mM TRIS, pH8.0), then mixing 2 microL of protein solution with 2 microL of well solution (0.1 M HEPES, pH 7.5, 2.0 M (NH4)2SO4).

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2016 / Details: collimator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.73→46.5 Å / Num. obs: 42552 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 74.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.037 / Rrim(I) all: 0.111 / Net I/σ(I): 12.6
Reflection shellResolution: 2.73→2.82 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 4132 / CC1/2: 0.587 / Rpim(I) all: 0.569 / Rrim(I) all: 1.583 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WOI

2woi


Resolution: 2.73→46.5 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.82
RfactorNum. reflection% reflection
Rfree0.2415 2064 4.85 %
Rwork0.196 --
obs0.1983 42552 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 84.7 Å2
Refinement stepCycle: LAST / Resolution: 2.73→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7472 0 251 19 7742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047896
X-RAY DIFFRACTIONf_angle_d0.61810730
X-RAY DIFFRACTIONf_dihedral_angle_d13.8344711
X-RAY DIFFRACTIONf_chiral_restr0.0441196
X-RAY DIFFRACTIONf_plane_restr0.0031345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7265-2.78990.42151350.33062647X-RAY DIFFRACTION100
2.7899-2.85970.33051190.31152670X-RAY DIFFRACTION100
2.8597-2.9370.33811240.30122643X-RAY DIFFRACTION100
2.937-3.02340.36811470.28682637X-RAY DIFFRACTION100
3.0234-3.1210.33941350.24632661X-RAY DIFFRACTION100
3.121-3.23250.31721300.24072658X-RAY DIFFRACTION100
3.2325-3.36190.29651230.22212700X-RAY DIFFRACTION100
3.3619-3.51490.27831260.21052679X-RAY DIFFRACTION100
3.5149-3.70010.26591430.19382654X-RAY DIFFRACTION100
3.7001-3.93180.22151520.18312707X-RAY DIFFRACTION100
3.9318-4.23520.21341360.1692695X-RAY DIFFRACTION100
4.2352-4.66110.19211560.14832693X-RAY DIFFRACTION100
4.6611-5.33480.18781270.15342755X-RAY DIFFRACTION100
5.3348-6.71830.25191400.20772772X-RAY DIFFRACTION100
6.7183-47.52740.21341710.18412919X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 31.8884 Å / Origin y: -13.0406 Å / Origin z: 6.9739 Å
111213212223313233
T0.5044 Å20.0883 Å20.0239 Å2-0.5287 Å20.0359 Å2--0.5163 Å2
L0.6527 °2-0.3098 °2-0.2822 °2-1.2406 °20.5307 °2--0.779 °2
S-0.0658 Å °-0.1631 Å °-0.0966 Å °0.1343 Å °0.0431 Å °-0.2787 Å °0.3005 Å °0.1849 Å °0.0328 Å °
Refinement TLS groupSelection details: all

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