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- PDB-2yau: X-ray structure of the Leishmania infantum tryopanothione reducta... -

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Basic information

Entry
Database: PDB / ID: 2yau
TitleX-ray structure of the Leishmania infantum tryopanothione reductase in complex with auranofin
ComponentsTRYPANOTHIONE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / cellular response to oxidative stress / flavin adenine dinucleotide binding / mitochondrion / 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-NDP / Chem-TS8 / Trypanothione reductase
Similarity search - Component
Biological speciesLEISHMANIA INFANTUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBaiocco, P. / Ilari, A. / Colotti, G.
CitationJournal: Amino Acids / Year: 2012
Title: A Gold-Containing Drug Against Parasitic Polyamine Metabolism: The X-Ray Structure of Trypanothione Reductase from Leishmania Infantum in Complex with Auranofin Reveals a Dual Mechanism of Enzyme Inhibition.
Authors: Ilari, A. / Baiocco, P. / Messori, L. / Fiorillo, A. / Boffi, A. / Gramiccia, M. / Di Muccio, T. / Colotti, G.
History
DepositionFeb 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Other
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)114,96314
Polymers110,5152
Non-polymers4,44812
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-168.2 kcal/mol
Surface area35620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.058, 103.058, 191.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 1 - 488 / Label seq-ID: 21 - 508

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.00036, -1, 0.00097), (-1, 0.00036, 0.00031), (-0.00031, -0.00097, -1)
Vector: -51.54671, -51.50475, 0.06896)

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein TRYPANOTHIONE REDUCTASE


Mass: 55257.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA INFANTUM (eukaryote) / Plasmid: PET28-6H-TR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4HSF7, trypanothione-disulfide reductase
#5: Sugar ChemComp-TS8 / 2,3,4,6-tetra-O-acetyl-1-thio-beta-D-glucopyranose / 3,4,5-TRIACETYLOXY-6-(ACETYLOXYMETHYL)OXANE-2-THIOL / 2,3,4,6-tetra-O-acetyl-1-thio-beta-D-glucose / 2,3,4,6-tetra-O-acetyl-1-thio-D-glucose / 2,3,4,6-tetra-O-acetyl-1-thio-glucose


Type: D-saccharide, beta linking / Mass: 364.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20O9S
IdentifierTypeProgram
b-D-Glcp1SH2Ac3Ac4Ac6AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 4.75 Å3/Da / Density % sol: 73.9 % / Description: NONE
Crystal growpH: 8.5 / Details: 2.2 M AMMONIUM SULFATE, 0.1 M TRIS BUFFER PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.975
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 25665 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 76.5 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.04

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JK6

2jk6


Resolution: 3.5→50 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.844 / SU B: 40.585 / SU ML: 0.579 / Cross valid method: THROUGHOUT / ESU R: 2.732 / ESU R Free: 0.644 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31912 1291 5.1 %RANDOM
Rwork0.26704 ---
obs0.26972 23884 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.961 Å2
Baniso -1Baniso -2Baniso -3
1-4.68 Å20 Å20 Å2
2--4.68 Å20 Å2
3----9.36 Å2
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7388 0 264 0 7652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227818
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.99610620
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38524.331314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.06151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7721538
X-RAY DIFFRACTIONr_chiral_restr0.0850.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3694 / Refine-ID: X-RAY DIFFRACTION / Type: medium positional / Rms dev position: 0.3 Å / Weight position: 0.5

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 108 -
Rwork0.397 1732 -
obs--99.89 %

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