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

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Entry
Database: PDB / ID: 1grb
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 / Detoxification of Reactive Oxygen Species / Nuclear events mediated by NFE2L2 / cell redox homeostasis / glutathione metabolic process / TP53 Regulates Metabolic Genes / cellular response to oxidative stress ...glutathione-disulfide reductase / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / glutathione-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / Detoxification of Reactive Oxygen Species / Nuclear events mediated by NFE2L2 / cell redox homeostasis / glutathione metabolic process / TP53 Regulates Metabolic Genes / cellular response to oxidative stress / flavin adenine dinucleotide binding / NADP binding / 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 oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Glutathione reductase, eukaryote/bacterial / Pyridine nucleotide-disulphide oxidoreductase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, C-terminal 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Chem-NDP / Glutathione reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.85 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, 1992-
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

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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)53,9265
Polymers51,6361
Non-polymers2,2894
Water9,494527
1
A: GLUTATHIONE REDUCTASE
hetero molecules

A: GLUTATHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,85110
Polymers103,2722
Non-polymers4,5798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area15150 Å2
ΔGint-96 kcal/mol
Surface area35460 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.
2: MODEL OF NADPH BOUND TO GLUTATHIONE REDUCTASE AS COMPOSED OF NADH AND 2',5'-ADP ACCORDING TO KARPLUS & SCHULZ, J. MOL. BIOL. 210, 163-180 (1989)

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 531 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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 grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Common name: ammonium sulfate

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.85→10 Å / σ(F): 0
Details: THE ENZYME CRYSTAL WAS SOAKED WITH NADH, DATA WERE COLLECTED, AND THE STRUCTURE OF THE REDUCED ENZYME WITH BOUND NADH WAS REFINED. THE CRYSTAL STRUCTURE NAME IN THE PUBLICATION IS E2:NADH.
RfactorNum. reflection
obs0.162 38343
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 150 527 4176

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