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- PDB-2zz0: Crystal structure of human thioredoxin reductase I (SeCys 498 Cys) -

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Basic information

Entry
Database: PDB / ID: 2zz0
TitleCrystal structure of human thioredoxin reductase I (SeCys 498 Cys)
ComponentsThioredoxin reductase 1, cytoplasmic
KeywordsOXIDOREDUCTASE / Rossmann fold / Alternative splicing / Cytoplasm / Electron transport / FAD / Flavoprotein / NADP / Nucleus / Phosphoprotein / Polymorphism / Redox-active center / Selenium / Selenocysteine / Transport
Function / homology
Function and homology information


Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin ...Metabolism of ingested MeSeO2H into MeSeH / NADPH peroxidase / NADPH peroxidase activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / thioredoxin-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Uptake and function of diphtheria toxin / Detoxification of Reactive Oxygen Species / mesoderm formation / FAD binding / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / PPARA activates gene expression / fibrillar center / cellular response to oxidative stress / cell population proliferation / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / 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 ...Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / 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 / Thioredoxin-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase 1, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLo, Y.C. / Ko, T.P. / Wang, A.H.J.
CitationJournal: J.Inorg.Biochem. / Year: 2009
Title: Terpyridine-platinum(II) complexes are effective inhibitors of mammalian topoisomerases and human thioredoxin reductase 1.
Authors: Lo, Y.C. / Ko, T.P. / Su, W.C. / Su, T.L. / Wang, A.H.J.
History
DepositionFeb 2, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Dec 4, 2019Group: Database references / Non-polymer description / Structure summary
Category: chem_comp / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase 1, cytoplasmic
B: Thioredoxin reductase 1, cytoplasmic
C: Thioredoxin reductase 1, cytoplasmic
D: Thioredoxin reductase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,48812
Polymers225,9614
Non-polymers3,5268
Water9,548530
1
A: Thioredoxin reductase 1, cytoplasmic
B: Thioredoxin reductase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7446
Polymers112,9812
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-64 kcal/mol
Surface area38920 Å2
MethodPISA
2
C: Thioredoxin reductase 1, cytoplasmic
D: Thioredoxin reductase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7446
Polymers112,9812
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-57 kcal/mol
Surface area38870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.086, 135.414, 345.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

21B-500-

HOH

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Components

#1: Protein
Thioredoxin reductase 1, cytoplasmic / TR / Thioredoxin reductase TR1 / KM-102-derived reductase-like factor / Gene associated with ...TR / Thioredoxin reductase TR1 / KM-102-derived reductase-like factor / Gene associated with retinoid-IFN-induced mortality 12 protein / GRIM-12


Mass: 56490.328 Da / Num. of mol.: 4 / Fragment: residues (-13)-499 / Mutation: SeCys498Cys
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXNRD1, KDRF / Plasmid: pET46 EK/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q16881, thioredoxin-disulfide reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSWISSPROT SHOWS SELENOCYSTEINE AT THIS POSITION. THE AUTHOR STATES THERE IS MUTATION SECYS 498 CYS

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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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5% PEG 3350, 0.005M magnesium Sulfate, 0.05M MES, pH 6.0, 20% 1,6 Hexanediol (0.001mL), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2007 / Details: mirrors
RadiationMonochromator: Si 111 chennel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 70448 / Num. obs: 66151 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6542 / % possible all: 94.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CFY

2cfy


Resolution: 2.8→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3229 -Random
Rwork0.22 ---
all0.223 63859 --
obs0.223 60630 91 %-
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15056 0 232 530 15818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_bond_d0.02
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.0481
RfactorNum. reflection% reflection
Rfree0.4142 297 -
Rwork0.3661 --
obs-5925 85.27 %

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