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- PDB-4acs: Crystal structure of mutant GST A2-2 with enhanced catalytic effi... -

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Basic information

Entry
Database: PDB / ID: 4acs
TitleCrystal structure of mutant GST A2-2 with enhanced catalytic efficiency with azathioprine
ComponentsGLUTATHIONE S-TRANSFERASE A2
KeywordsTRANSFERASE / OXIDATION-REDUCTION
Function / homology
Function and homology information


Glutathione conjugation / Azathioprine ADME / glutathione transferase / glutathione transferase activity / epithelial cell differentiation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / xenobiotic metabolic process / glutathione metabolic process / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-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, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-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
GLUTATHIONE / Glutathione S-transferase A2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, W. / Moden, O. / Tars, K. / Mannervik, B.
CitationJournal: Chem.Biol. / Year: 2012
Title: Structure-based redesign of GST A2-2 for enhanced catalytic efficiency with azathioprine.
Authors: Zhang, W. / Moden, O. / Tars, K. / Mannervik, B.
History
DepositionDec 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Other
Revision 1.2May 2, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow / pdbx_database_status
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: GLUTATHIONE S-TRANSFERASE A2
B: GLUTATHIONE S-TRANSFERASE A2
C: GLUTATHIONE S-TRANSFERASE A2
D: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7408
Polymers102,5114
Non-polymers1,2294
Water9,278515
1
A: GLUTATHIONE S-TRANSFERASE A2
B: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8704
Polymers51,2552
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-28.2 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE A2
D: GLUTATHIONE S-TRANSFERASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8704
Polymers51,2552
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-27.5 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.660, 94.800, 113.720
Angle α, β, γ (deg.)90.00, 92.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.95616, 0.26033, -0.13412), (0.2608, -0.96529, -0.01434), (-0.1332, -0.02126, -0.99086)13.4721, -88.97284, 23.69151
2given(-0.95781, -0.25488, 0.13281), (0.25506, -0.96679, -0.01595), (0.13246, 0.01859, 0.99101)-29.57238, -41.21671, -10.30062
3given(-0.99998, -0.00593, 0.0025), (-0.00592, 0.99998, 0.0007), (-0.0025, 0.00069, -1)-16.61566, 47.59628, 13.53473

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE A2 / GST HA SUBUNIT 2 / GST CLASS-ALPHA MEMBER 2 / GST-GAMMA / GSTA2-2 / GTH2


Mass: 25627.738 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE / References: UniProt: P09210, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 107 TO GLY ENGINEERED RESIDUE IN CHAIN A, LEU 108 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, LEU 107 TO GLY ENGINEERED RESIDUE IN CHAIN A, LEU 108 TO ASP ENGINEERED RESIDUE IN CHAIN A, PHE 222 TO HIS ENGINEERED RESIDUE IN CHAIN B, LEU 107 TO GLY ENGINEERED RESIDUE IN CHAIN B, LEU 108 TO ASP ENGINEERED RESIDUE IN CHAIN B, PHE 222 TO HIS ENGINEERED RESIDUE IN CHAIN C, LEU 107 TO GLY ENGINEERED RESIDUE IN CHAIN C, LEU 108 TO ASP ENGINEERED RESIDUE IN CHAIN C, PHE 222 TO HIS ENGINEERED RESIDUE IN CHAIN D, LEU 107 TO GLY ENGINEERED RESIDUE IN CHAIN D, LEU 108 TO ASP ENGINEERED RESIDUE IN CHAIN D, PHE 222 TO HIS

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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: 2.6 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: CRYSTALS WERE GROWN BY HANING DROP METHOD BY MIXING EQUAL VOLUMES (4 UL) OF PROTEIN (10 MG/ML)AND GLUTATHIONE S-CONJUGATE (5 MM) MIXTURE AND RESERVOIR SOLUTION CONTAINING 9-14% PEG 4000 AND ...Details: CRYSTALS WERE GROWN BY HANING DROP METHOD BY MIXING EQUAL VOLUMES (4 UL) OF PROTEIN (10 MG/ML)AND GLUTATHIONE S-CONJUGATE (5 MM) MIXTURE AND RESERVOIR SOLUTION CONTAINING 9-14% PEG 4000 AND 2 MM DTT IN 100 MM TRIS-HCL (PH 7.8) WITH ADDITIONAL OCTYL D-BETA- GLUCOPYRANOSIDE TO A FINAL CONCENTRATION OF 0.1% (W/V)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Type: ESRF / Wavelength: 0.9334
DetectorDetector: CCD / Date: Jul 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.1→38 Å / Num. obs: 55710 / % possible obs: 93 % / Observed criterion σ(I): 2.6 / Redundancy: 3.2 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.1
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / % possible all: 77

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJU

2wju


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.831 / Cor.coef. Fo:Fc free: 0.756 / SU B: 7.732 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.32107 2820 5.1 %RANDOM
Rwork0.26117 ---
obs0.26425 52867 92.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.155 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å20 Å21.78 Å2
2---1.59 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7070 0 80 515 7665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027280
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5752.0089770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67724.506324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.135151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1791542
X-RAY DIFFRACTIONr_chiral_restr0.1060.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215354
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 141 -
Rwork0.267 3140 -
obs--74.55 %

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