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- PDB-1h6v: Mammalian thioredoxin reductase -

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Basic information

Entry
Database: PDB / ID: 1h6v
TitleMammalian thioredoxin reductase
ComponentsTHIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / PYRIDINE NUCLEOTIDE-DISULFIDE OXIDOREDUCTASE / FLAVOPROTEIN
Function / homology
Function and homology information


selenate reductase activity / halogen metabolic process / Metabolism of ingested MeSeO2H into MeSeH / benzene-containing compound metabolic process / Interconversion of nucleotide di- and triphosphates / selenocysteine metabolic process / Detoxification of Reactive Oxygen Species / NADPH peroxidase / NADPH peroxidase activity / cellular response to hyperoxia ...selenate reductase activity / halogen metabolic process / Metabolism of ingested MeSeO2H into MeSeH / benzene-containing compound metabolic process / Interconversion of nucleotide di- and triphosphates / selenocysteine metabolic process / Detoxification of Reactive Oxygen Species / NADPH peroxidase / NADPH peroxidase activity / cellular response to hyperoxia / TP53 Regulates Metabolic Genes / NADPH oxidation / mercury ion binding / NAD(P)H oxidase H2O2-forming activity / thioredoxin-disulfide reductase / response to selenium ion / thioredoxin-disulfide reductase (NADPH) activity / mesoderm formation / gastrulation / response to axon injury / response to hyperoxia / cellular response to copper ion / FAD binding / cell redox homeostasis / hydrogen peroxide catabolic process / placenta development / response to oxidative stress / cell population proliferation / response to xenobiotic stimulus / positive regulation of apoptotic process / neuronal cell body / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / 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 ...Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / 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 / Thioredoxin reductase 1, cytoplasmic
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSandalova, T. / Zhong, L. / Lindqvist, Y. / Holmgren, A. / Schneider, G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Three-Dimensional Structure of a Mammalian Thioredoxin Reductase: Implication for Mechanism and Evolution of a Selenocysteine Dependent Enzyme
Authors: Sandalova, T. / Zhong, L. / Lindqvist, Y. / Holmgren, A. / Schneider, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Purification, Crystallization and Preliminarycrystallographic Data for Rat Cytosolic Selenocysteine 498 - Cysteine Mutant Thioredoxin Reductase
Authors: Zhong, L. / Persson, K. / Sandalova, T. / Schneider, G. / Holmgren, A.
History
DepositionJun 27, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN REDUCTASE
B: THIOREDOXIN REDUCTASE
C: THIOREDOXIN REDUCTASE
D: THIOREDOXIN REDUCTASE
E: THIOREDOXIN REDUCTASE
F: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,06418
Polymers327,8786
Non-polymers9,18612
Water1629
1
A: THIOREDOXIN REDUCTASE
B: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3556
Polymers109,2932
Non-polymers3,0624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: THIOREDOXIN REDUCTASE
D: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3556
Polymers109,2932
Non-polymers3,0624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: THIOREDOXIN REDUCTASE
F: THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3556
Polymers109,2932
Non-polymers3,0624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.920, 140.464, 170.832
Angle α, β, γ (deg.)90.00, 94.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.574136, -0.81876, -0.000551), (-0.818756, 0.574132, 0.003328), (-0.002409, 0.002362, -0.999994)22.216, 11.037, 271.048
2given(-0.357321, -0.923981, -0.136313), (0.923651, -0.371232, 0.09516), (-0.138529, -0.091903, 0.986085)22.729, 27.48, 59.201
3given(0.961212, -0.239856, 0.136163), (-0.229693, -0.969436, -0.08623), (0.152684, 0.05161, -0.986926)-13.447, 9.338, 211.873
4given(-0.441708, 0.894327, 0.071221), (0.897158, 0.44037, 0.034371), (-0.000625, 0.079079, -0.996868)18.319, -17.455, 155.05099
5given(-0.469996, 0.879989, -0.068722), (-0.87986, -0.473284, -0.042995), (-0.07036, 0.040258, 0.996709)25.657, -13.668, 116.038

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Components

#1: Protein
THIOREDOXIN REDUCTASE /


Mass: 54646.305 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell line: PC-12 / Plasmid: PET-3D TRXRU498C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O89049, EC: 1.6.4.5
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C, D, E, F ENGINEERED MUTATION SECYS498CYS

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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: 2.86 Å3/Da / Density % sol: 56.65 %
Crystal growpH: 7.5
Details: 20% PEG 8000 IN 50MM POTASSIUM PHOSPHATE, PH 5.0 AND 2MM OF NADP+
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Zhong, L., (2000) Acta Crystallogr.,Sect.D, 56, 1191.
Components of the solutions
*PLUS
Conc.: 60 mg/ml / Common name: enzyme

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.104
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.104 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 69351 / % possible obs: 92.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 7 / % possible all: 77.6
Reflection
*PLUS
Num. measured all: 212337
Reflection shell
*PLUS
% possible obs: 77.6 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GRA

1gra


Resolution: 3→30 Å / SU B: 20.412 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / Details: CHAINS A, B, E, AND F ARE BETTER
RfactorNum. reflection% reflectionSelection details
Rfree0.26295 3441 5 %RANDOM
Rwork0.22357 ---
obs0.22555 65887 92.41 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22514 0 552 9 23075
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_d1.97

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