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- PDB-5grt: HUMAN GLUTATHIONE REDUCTASE A34E, R37W MUTANT, GLUTATHIONYLSPERMI... -

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Basic information

Entry
Database: PDB / ID: 5grt
TitleHUMAN GLUTATHIONE REDUCTASE A34E, R37W MUTANT, GLUTATHIONYLSPERMIDINE COMPLEX
ComponentsGLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / GLUTATHIONYL SPERMIDINE
Function / homology
Function and homology information


glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / flavin adenine dinucleotide binding ...glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / glutathione metabolic process / cell redox homeostasis / TP53 Regulates Metabolic Genes / flavin adenine dinucleotide binding / NADP binding / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / external side of plasma membrane / mitochondrion / extracellular exosome / cytosol
Similarity search - Function
Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / 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 ...Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / : / 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 / GLUTATHIONYLSPERMIDINE DISULFIDE / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIRECT BASED ON KNOWN MODEL / Resolution: 2.4 Å
AuthorsStoll, V.S. / Simpson, S.J. / Krauth-Siegel, R.L. / Walsh, C.T. / Pai, E.F.
Citation
Journal: Biochemistry / Year: 1997
Title: Glutathione reductase turned into trypanothione reductase: structural analysis of an engineered change in substrate specificity.
Authors: Stoll, V.S. / Simpson, S.J. / Krauth-Siegel, R.L. / Walsh, C.T. / Pai, E.F.
#1: Journal: Biochemistry / Year: 1991
Title: Redox Enzyme Engineering: Conversion of Human Glutathione Reductase Into a Trypanothione Reductase
Authors: Bradley, M. / Bucheler, U.S. / Walsh, C.T.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Refined Structure of Glutathione Reductase at 1.54 A Resolution
Authors: Karplus, P.A. / Schulz, G.E.
#3: Journal: J.Biol.Chem. / Year: 1983
Title: The Catalytic Mechanism of Glutathione Reductase as Derived from X-Ray Diffraction Analyses of Reaction Intermediates
Authors: Pai, E.F. / Schulz, G.E.
#4: Journal: J.Mol.Biol. / Year: 1983
Title: Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase
Authors: Wierenga, R.K. / Drenth, J. / Schulz, G.E.
#5: Journal: Eur.J.Biochem. / Year: 1982
Title: Glutathione Reductase from Human Erythrocytes. The Sequences of the Nadph Domain and of the Interface Domain
Authors: Krauth-Siegel, R.L. / Blatterspiel, R. / Saleh, M. / Schiltz, E. / Schirmer, R.H. / Untucht-Grau, R.
#6: Journal: J.Mol.Biol. / Year: 1982
Title: Fad-Binding Site of Glutathione Reductase
Authors: Schulz, G.E. / Schirmer, R.H. / Pai, E.F.
#7: Journal: J.Mol.Biol. / Year: 1981
Title: Three-Dimensional Structure of Glutathione Reductase at 2 A Resolution
Authors: Thieme, R. / Pai, E.F. / Schirmer, R.H. / Schulz, G.E.
#8: Journal: J.Mol.Biol. / Year: 1980
Title: Gene Duplication in Glutathione Reductase
Authors: Schulz, G.E.
#9: Journal: FEBS Lett. / Year: 1979
Title: The C-Terminal Fragment of Human Glutathione Reductase Contains the Postulated Catalytic Histidine
Authors: Untucht-Grau, R. / Schulz, G.E. / Schirmer, R.H.
#10: Journal: Nature / Year: 1978
Title: The Structure of the Flavoenzyme Glutathione Reductase
Authors: Schulz, G.E. / Schirmer, R.H. / Sachsenheimer, W. / Pai, E.F.
#11: Journal: J.Mol.Biol. / Year: 1977
Title: Low Resolution Structure of Human Erythrocyte Glutathione Reductase
Authors: Zappe, H.A. / Krohne-Ehrich, G. / Schulz, G.E.
#12: Journal: FEBS Lett. / Year: 1975
Title: Crystals of Human Erythrocyte Glutathione Reductase
Authors: Schulz, G.E. / Zappe, H. / Worthington, D.J. / Rosemeyer, M.A.
History
DepositionFeb 12, 1997Processing site: BNL
Revision 1.0Aug 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7183
Polymers50,0651
Non-polymers1,6532
Water00
1
A: GLUTATHIONE REDUCTASE
hetero molecules

A: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4366
Polymers100,1312
Non-polymers3,3054
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area12310 Å2
ΔGint-63 kcal/mol
Surface area35420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.120, 84.790, 63.650
Angle α, β, γ (deg.)90.00, 90.00, 58.41
Int Tables number5
Space group name H-MB112

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Components

#1: Protein GLUTATHIONE REDUCTASE / GRTR


Mass: 50065.480 Da / Num. of mol.: 1 / Mutation: A34E, R37W
Source method: isolated from a genetically manipulated source
Details: CONTAINS A NON-COVALENTLY BOUND FAD AND OXIDIZED GLUTATHIONYLSPERMIDINE SUBSTRATE
Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELLS / Organ: BLOOD / Plasmid: PUB302 / Production host: Escherichia coli (E. coli) / References: UniProt: P00390, EC: 1.6.4.2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-TS4 / GLUTATHIONYLSPERMIDINE DISULFIDE


Mass: 867.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H66N12O10S2
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growpH: 8
Details: 0.57-0.90 M AMMONIUM SULFATE, 100 MM POTASSIUM PHOSPHATE, PH 8.0, AND 0.5% 1-N-BETA-OCTYL-D-GLUCOPYRANOSIDE HANGING DROP VAPOR DIFFUSION, CRYSTAL SOAKED IN ARTIFICIAL MOTHER LIQUOR AT PH 8. ...Details: 0.57-0.90 M AMMONIUM SULFATE, 100 MM POTASSIUM PHOSPHATE, PH 8.0, AND 0.5% 1-N-BETA-OCTYL-D-GLUCOPYRANOSIDE HANGING DROP VAPOR DIFFUSION, CRYSTAL SOAKED IN ARTIFICIAL MOTHER LIQUOR AT PH 8.0,CONTAINING 0.5% BETA-OCTYL GLUCOSIDE AND 42 MM GLUTATHIONYLSPERMIDINE.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.57-0.59 Mammonium sulfate1drop
2100 mMpotassium phosphate1drop
30.5 %(w/v)1-n-octyl-beta-D-glucopyranoside1drop
40.57-0.59 Mammonium sulfate1reservoir
5100 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1992 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 16124 / % possible obs: 84.8 % / Observed criterion σ(I): 0.1 / Redundancy: 1.8 % / Rsym value: 0.056
Reflection shellResolution: 2.4→2.53 Å / % possible all: 40.9
Reflection
*PLUS
Num. measured all: 29646 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 40.9 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: DIRECT BASED ON KNOWN MODEL
Starting model: PDB ENTRY 1GRT

1grt


Resolution: 2.4→10 Å / Data cutoff high absF: 10000000 / σ(F): 0.1
RfactorNum. reflection% reflection
Rwork0.197 --
obs0.197 16122 75.2 %
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 111 0 3617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.42
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.197 1205 -
obs--40.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2FN3.PARMTOPH19.PEP
X-RAY DIFFRACTION3GSP.PARMGSP.TOP
X-RAY DIFFRACTION4FN3.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16124
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.42
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.67
LS refinement shell
*PLUS
Rfactor obs: 0.197

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