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- PDB-5bzx: Crystal structure of human phosphatase PTEN treated with a bisper... -

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Basic information

Entry
Database: PDB / ID: 5bzx
TitleCrystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
KeywordsHYDROLASE / phosphatase / C2 domain / disulfide / oxidized / vanadate
Function / homology
Function and homology information


PTEN Loss of Function in Cancer / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / negative regulation of peptidyl-serine phosphorylation / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity ...PTEN Loss of Function in Cancer / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / negative regulation of peptidyl-serine phosphorylation / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / Negative regulation of the PI3K/AKT network / synapse maturation / negative regulation of cell cycle G1/S phase transition / Regulation of PTEN mRNA translation / myelin sheath adaxonal region / cellular response to electrical stimulus / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / presynaptic membrane assembly / negative regulation of axonogenesis / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / Transcriptional Regulation by MECP2 / negative regulation of organ growth / forebrain morphogenesis / negative regulation of focal adhesion assembly / phosphatidylinositol dephosphorylation / negative regulation of excitatory postsynaptic potential / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / anaphase-promoting complex binding / Schmidt-Lanterman incisure / dentate gyrus development / ubiquitin ligase activator activity / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / maternal behavior / spindle assembly involved in female meiosis / negative regulation of cell size / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of epithelial to mesenchymal transition / molecular function inhibitor activity / protein-serine/threonine phosphatase / negative regulation of G1/S transition of mitotic cell cycle / regulation of neuron projection development / ubiquitin-specific protease binding / protein serine/threonine phosphatase activity / Synthesis of IP3 and IP4 in the cytosol / locomotor rhythm / Synthesis of PIPs at the plasma membrane / adult behavior / positive regulation of intracellular signal transduction / negative regulation of vascular associated smooth muscle cell proliferation / phosphoprotein phosphatase activity / negative regulation of cellular senescence / social behavior / positive regulation of excitatory postsynaptic potential / negative regulation of osteoblast differentiation / multicellular organismal response to stress / prepulse inhibition / protein dephosphorylation / synapse assembly / protein-tyrosine-phosphatase / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tyrosine phosphatase activity / Regulation of PTEN localization / negative regulation of cell migration / central nervous system development / cell projection / PDZ domain binding / TP53 Regulates Metabolic Genes / locomotory behavior / cell motility / phosphatidylinositol 3-kinase/protein kinase B signal transduction / beta-catenin binding / PML body / regulation of protein stability / cytoplasmic side of plasma membrane / Regulation of PTEN stability and activity / Ovarian tumor domain proteases / Downstream TCR signaling / cell migration / negative regulation of neuron projection development / heart development / dendritic spine / learning or memory / neuron projection / Ub-specific processing proteases / protein stabilization / postsynaptic density / apical plasma membrane / negative regulation of cell population proliferation / apoptotic process / positive regulation of cell population proliferation / lipid binding / enzyme binding / positive regulation of transcription by RNA polymerase II
Similarity search - Function
Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / Immunoglobulin-like - #1110 / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. ...Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / Immunoglobulin-like - #1110 / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / VANADATE ION / Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLee, C.-U. / Bier, D. / Hennig, S. / Grossmann, T.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGR3592/2-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Redox Modulation of PTEN Phosphatase Activity by Hydrogen Peroxide and Bisperoxidovanadium Complexes.
Authors: Lee, C.U. / Hahne, G. / Hanske, J. / Bange, T. / Bier, D. / Rademacher, C. / Hennig, S. / Grossmann, T.N.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.1Nov 20, 2024Group: Structure summary / Category: 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: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
B: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
C: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
D: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9119
Polymers149,2314
Non-polymers6805
Water15,853880
1
A: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4232
Polymers37,3081
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4582
Polymers37,3081
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5733
Polymers37,3081
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4582
Polymers37,3081
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)207.060, 206.900, 87.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

21A-522-

HOH

31A-624-

HOH

41C-620-

HOH

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Components

#1: Protein
Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / Mutated in multiple advanced cancers 1 / Phosphatase and tensin homolog


Mass: 37307.805 Da / Num. of mol.: 4 / Fragment: PTEN wt 7-353 delta 286-309 / Mutation: Deletion 286-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTEN, MMAC1, TEP1 / Plasmid: pFH1
Details (production host): Bacmid DNA derived from pFH1 transformed in DH10Bac E. coli
Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase
#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.77119 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77119 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11K, H, -L20.499
ReflectionResolution: 2.5→46.293 Å / Num. obs: 65393 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.91 % / Biso Wilson estimate: 56.698 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.123 / Χ2: 0.949 / Net I/σ(I): 17.43 / Num. measured all: 843899
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.60.7311.5521.5387652714771451.619100
2.6-2.70.8511.12.2577080614461421.147100
2.7-2.80.9210.8193.0467403534153410.854100
2.8-2.90.960.5764.3458498459145900.6100
2.9-30.9780.4245.7149248404940490.442100
3-3.10.980.3796.5642575349734960.396100
3.1-40.9980.1318.5124842618312183110.135100
4-60.9990.05539.8614957111341113410.057100
6-80.9990.05139.7335011283328320.054100
8-1010.03457.6913692102410240.036100
10-1510.03565.55107157787780.036100
15-2010.03959.4324761921920.041100
2010.03552.5115521671520.03791

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7 Å46.29 Å
Translation7 Å46.29 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1d5r

1d5r


Resolution: 2.5→46.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1852 / WRfactor Rwork: 0.1601 / FOM work R set: 0.8448 / SU B: 4.673 / SU ML: 0.111 / SU R Cruickshank DPI: 0.0763 / SU Rfree: 0.0467 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3297 5 %RANDOM
Rwork0.1752 ---
obs0.1767 62095 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.99 Å2 / Biso mean: 59.842 Å2 / Biso min: 29.37 Å2
Baniso -1Baniso -2Baniso -3
1--33.11 Å20 Å20 Å2
2---30.39 Å20 Å2
3---63.5 Å2
Refinement stepCycle: final / Resolution: 2.5→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10310 0 40 880 11230
Biso mean--55.13 57.52 -
Num. residues----1256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910650
X-RAY DIFFRACTIONr_bond_other_d0.0060.029820
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.95214409
X-RAY DIFFRACTIONr_angle_other_deg1.451322568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.4651252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76223.499543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.237151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5341562
X-RAY DIFFRACTIONr_chiral_restr0.0880.21488
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112052
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022672
X-RAY DIFFRACTIONr_mcbond_it3.556.1095020
X-RAY DIFFRACTIONr_mcbond_other3.5496.1085019
X-RAY DIFFRACTIONr_mcangle_it5.6669.1636268
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 231 -
Rwork0.342 4369 -
all-4600 -
obs--96.27 %

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