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- PDB-1fw1: Glutathione transferase zeta/maleylacetoacetate isomerase -

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Basic information

Entry
Database: PDB / ID: 1fw1
TitleGlutathione transferase zeta/maleylacetoacetate isomerase
ComponentsGLUTATHIONE TRANSFERASE ZETA
KeywordsISOMERASE/TRANSFERASE / glutathione transferase / ISOMERASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


maleylacetoacetate isomerase / Tyrosine catabolism / maleylacetoacetate isomerase activity / tyrosine catabolic process / Glutathione conjugation / L-phenylalanine catabolic process / Regulation of pyruvate dehydrogenase (PDH) complex / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity ...maleylacetoacetate isomerase / Tyrosine catabolism / maleylacetoacetate isomerase activity / tyrosine catabolic process / Glutathione conjugation / L-phenylalanine catabolic process / Regulation of pyruvate dehydrogenase (PDH) complex / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / mitochondrial matrix / protein homodimerization activity / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta , N-terminal / Glutathione S-transferases, class Zeta / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ...Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta , N-terminal / Glutathione S-transferases, class Zeta / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / GLUTATHIONE / Maleylacetoacetate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsPolekhina, G. / Board, P.G. / Blackburn, A.C. / Parker, M.W.
Citation
Journal: Biochemistry / Year: 2001
Title: Crystal structure of maleylacetoacetate isomerase/glutathione transferase zeta reveals the molecular basis for its remarkable catalytic promiscuity.
Authors: Polekhina, G. / Board, P.G. / Blackburn, A.C. / Parker, M.W.
#1: Journal: Cytogenet.Cell Genet. / Year: 1998
Title: Characterization and chromosome location of the gene GSTZ1 encoding the human Zeta class glutathione transferase and maleylacetoacetate isomerase
Authors: Blackburn, A.C. / Woollatt, E. / Sutherland, G.R. / Board, P.G.
#2: Journal: Biochem.J. / Year: 1998
Title: Glutathione transferase Zeta catalyses the oxygenation of the carcinogen dichloroacetic acid to glyoxylic acid
Authors: Tong, Z. / Board, P.G. / Anders, M.W.
History
DepositionSep 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE TRANSFERASE ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6664
Polymers24,1081
Non-polymers5583
Water1,964109
1
A: GLUTATHIONE TRANSFERASE ZETA
hetero molecules

A: GLUTATHIONE TRANSFERASE ZETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3318
Polymers48,2162
Non-polymers1,1156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5640 Å2
ΔGint-91 kcal/mol
Surface area16970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.000, 100.000, 56.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

21A-327-

HOH

DetailsThe biological assembly is a dimer. The dimer can be created from monomer A through the crystallographic 2-fold axis. The symmetry operation to be used is y,x,-z.

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Components

#1: Protein GLUTATHIONE TRANSFERASE ZETA / MALEYLACETOACETATE ISOMERASE


Mass: 24107.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: O43708, maleylacetoacetate isomerase, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: ammonium sulfate, tert-butanol, bicine, glutathione, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K, temperature 295K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMHEPES1drop
22 mMdithiothreitol1drop
32 mMGSH1drop
410 mg/mlprotein1drop
5100 mMBicine1reservoir
610 mMdithiothreitol1reservoir
710 mMGSH1reservoir
848-52 %satammonium sulfate1reservoir
91 %tert-butyl alcohol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 22750 / Num. obs: 152479 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 35.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.286 / Num. unique all: 1340 / % possible all: 88.7
Reflection
*PLUS
Num. obs: 22750 / Num. measured all: 152479
Reflection shell
*PLUS
Mean I/σ(I) obs: 7.4

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→28.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1875438.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2317 10.2 %RANDOM
Rwork0.234 ---
all0.234 22697 --
obs0.234 22697 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.05 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--17.76 Å20 Å20 Å2
2---17.76 Å20 Å2
3---35.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 33 109 1772
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.322.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.463 341 10.3 %
Rwork0.439 2977 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GSH_1.PARGSH_1.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.21
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.463 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.439

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