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- PDB-1gra: SUBSTRATE BINDING AND CATALYSIS BY GLUTATHIONE REDUCTASE AS DERIV... -

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Entry
Database: PDB / ID: 1gra
TitleSUBSTRATE BINDING AND CATALYSIS BY GLUTATHIONE REDUCTASE AS DERIVED FROM REFINED ENZYME: SUBSTRATE CRYSTAL STRUCTURES AT 2 ANGSTROMS RESOLUTION
ComponentsGLUTATHIONE REDUCTASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE(FLAVOENZYME)
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 / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / GLUTATHIONE / Chem-NDP / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKarplus, P.A. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: substrate crystal structures at 2 A resolution.
Authors: Karplus, P.A. / Schulz, G.E.
#1: Journal: Eur.J.Biochem. / Year: 1988
Title: Inhibition of Human Glutathione Reductase by the Nitrosourea Drugs 1,3-Bis(2-Chloroethyl)-1-Nitrosourea and 1-(2-Chloroethyl)-3-(2-Hydroxyethyl)-1-Nitrosourea
Authors: Karplus, P.A. / Krauth-Siegel, R.L. / Schirmer, R.H. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Refined Structure of Glutathione Reductase at 1.54 Angstroms Resolution
Authors: Karplus, P.A. / Schulz, G.E.
#3: Journal: Eur.J.Biochem. / Year: 1984
Title: Interaction of a Glutathione S-Conjugate with Glutathione Reductase. Kinetic and X-Ray Crystallographic Studies
Authors: Bilzer, M. / Krauth-Siegel, R.L. / Schirmer, R.H. / Akerboom, T.P.M. / Sies, H. / 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: 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.
#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: 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.
#8: Journal: J.Mol.Biol. / Year: 1981
Title: Three-Dimensional Structure of Glutathione Reductase at 2 Angstroms Resolution
Authors: Thieme, R. / Pai, E.F. / Schirmer, R.H. / Schulz, G.E.
#9: Journal: J.Mol.Biol. / Year: 1980
Title: Gene Duplication in Glutathione Reductase
Authors: Schulz, G.E.
#10: 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.
#11: Journal: Nature / Year: 1978
Title: The Structure of the Flavoenzyme Glutathione Reductase
Authors: Schulz, G.E. / Schirmer, R.H. / Sachsenheimer, W. / Pai, E.F.
#12: 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.
#13: 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
DepositionDec 15, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jun 5, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7825
Polymers51,6361
Non-polymers2,1464
Water9,548530
1
A: GLUTATHIONE REDUCTASE
hetero molecules

A: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,56410
Polymers103,2722
Non-polymers4,2918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area13990 Å2
ΔGint-88 kcal/mol
Surface area35570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.800, 84.500, 63.200
Angle α, β, γ (deg.)90.00, 90.00, 58.70
Int Tables number5
Space group name H-MB112
Atom site foot note1: RESIDUES PRO 375 AND PRO 468 ARE CIS PROLINES.

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Components

#1: Protein GLUTATHIONE REDUCTASE


Mass: 51636.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growDetails: THE ENZYME CRYSTAL WAS SOAKED WITH GSSG AND NADP+, DATA WERE COLLECTED, AND THE STRUCTURE OF THE OXIDIZED ENZYME WITH BOUND GSSG AND NADP+ WAS REFINED. THE STRUCTURE CONTAINS 530 WATER ...Details: THE ENZYME CRYSTAL WAS SOAKED WITH GSSG AND NADP+, DATA WERE COLLECTED, AND THE STRUCTURE OF THE OXIDIZED ENZYME WITH BOUND GSSG AND NADP+ WAS REFINED. THE STRUCTURE CONTAINS 530 WATER MOLECULES, 38 DELETED IN RELATION TO FILE 3GRS, 45 ADDED IN RELATION TO FILE 3GRS.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Common name: ammonium sulfate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2→10 Å / σ(F): 0 / Details: THE CRYSTAL STRUCTURE NAME IS E0:GSSG:NADP+. /
RfactorNum. reflection
obs0.157 36228
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 120 530 4149

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