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- PDB-6zz4: Crystal structure of the PTPN2 C216G mutant -

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Basic information

Entry
Database: PDB / ID: 6zz4
TitleCrystal structure of the PTPN2 C216G mutant
ComponentsTyrosine-protein phosphatase non-receptor type 2
KeywordsSIGNALING PROTEIN / Phosphatase
Function / homology
Function and homology information


negative regulation of interleukin-2-mediated signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / negative regulation of positive thymic T cell selection / positive regulation of PERK-mediated unfolded protein response / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / negative regulation of macrophage differentiation / regulation of type II interferon-mediated signaling pathway / negative regulation of chemotaxis ...negative regulation of interleukin-2-mediated signaling pathway / negative regulation of interleukin-4-mediated signaling pathway / negative regulation of positive thymic T cell selection / positive regulation of PERK-mediated unfolded protein response / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of interleukin-6-mediated signaling pathway / negative regulation of macrophage differentiation / regulation of type II interferon-mediated signaling pathway / negative regulation of chemotaxis / negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / Interleukin-37 signaling / syntaxin binding / negative regulation of T cell receptor signaling pathway / negative regulation of type I interferon-mediated signaling pathway / STAT family protein binding / regulation of hepatocyte growth factor receptor signaling pathway / insulin receptor recycling / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of type II interferon-mediated signaling pathway / negative regulation of lipid storage / non-membrane spanning protein tyrosine phosphatase activity / endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation / peptidyl-tyrosine dephosphorylation / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of IFNG signaling / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / B cell differentiation / protein-tyrosine-phosphatase / erythrocyte differentiation / protein tyrosine phosphatase activity / endosome lumen / PKR-mediated signaling / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / negative regulation of inflammatory response / integrin binding / insulin receptor signaling pathway / glucose homeostasis / negative regulation of cell population proliferation / protein kinase binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-1/2 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain ...Protein-tyrosine phosphatase, non-receptor type-1/2 / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsMechaly, A.E. / Berthelet, J. / Nian, Q. / Parlato, M. / Cerf-Bensussan, N. / Haouz, A. / Rodrigues-Lima, F.
CitationJournal: Protein Sci. / Year: 2022
Title: Structural characterization of a pathogenic mutant of human protein tyrosine phosphatase PTPN2 (Cys216Gly) that causes very early onset autoimmune enteropathy.
Authors: Nian, Q. / Berthelet, J. / Parlato, M. / Mechaly, A.E. / Liu, R. / Dupret, J.M. / Cerf-Bensussan, N. / Haouz, A. / Rodrigues Lima, F.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 2
B: Tyrosine-protein phosphatase non-receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7958
Polymers73,2252
Non-polymers5706
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-39 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.890, 55.980, 101.420
Angle α, β, γ (deg.)90.000, 120.740, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 2 - 277 / Label seq-ID: 2 - 277

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 2 through 278)AA
22chain 'B'BB

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 2 / T-cell protein-tyrosine phosphatase / TCPTP


Mass: 36612.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN2, PTPT / Production host: Escherichia coli (E. coli) / References: UniProt: P17706, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M Tris HCl pH 8.5, 2 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.43→48.71 Å / Num. obs: 25798 / % possible obs: 98.23 % / Redundancy: 6.9 % / Biso Wilson estimate: 45.5 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1178 / Rpim(I) all: 0.04844 / Rrim(I) all: 0.1276 / Net I/σ(I): 10.97
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6404 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 2471 / CC1/2: 0.872 / CC star: 0.965 / Rpim(I) all: 0.2632 / Rrim(I) all: 0.6936 / % possible all: 94.26

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
BUSTERrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8K

1l8k


Resolution: 2.43→48.71 Å / SU ML: 0.3267 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.1927
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1288 5 %RANDOM
Rwork0.198 24483 --
obs0.2008 25771 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.21 Å2
Refinement stepCycle: LAST / Resolution: 2.43→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 30 173 4758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814691
X-RAY DIFFRACTIONf_angle_d1.03696358
X-RAY DIFFRACTIONf_chiral_restr0.0562679
X-RAY DIFFRACTIONf_plane_restr0.0074820
X-RAY DIFFRACTIONf_dihedral_angle_d5.6234614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.530.31281360.24272597X-RAY DIFFRACTION94.73
2.53-2.640.34551420.23642701X-RAY DIFFRACTION97.83
2.64-2.780.3271420.24262689X-RAY DIFFRACTION98.44
2.78-2.960.29181430.22632722X-RAY DIFFRACTION98.66
2.96-3.190.27021430.20362715X-RAY DIFFRACTION98.65
3.19-3.510.23991450.19082741X-RAY DIFFRACTION98.73
3.51-4.010.26391430.18132720X-RAY DIFFRACTION99.03
4.01-5.060.20771460.16492771X-RAY DIFFRACTION99.15
5.06-48.710.23591480.21272827X-RAY DIFFRACTION98.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.095986554870.04161792290330.6546623481930.9732784287210.4840602415063.70122637919-0.0613888596014-0.4486075460540.095579561920.03959476903170.02567511660890.120094662151-0.0120822070466-0.637914685250.03672961702670.2413352958210.02856819364590.007285587849980.387996910087-0.001674491101850.403246781543-20.6089427936-21.3960846192-4.96643442582
21.887540510660.4545070836910.5167925891232.207332124390.4492349410243.217382789260.0500372462670.0975001152158-0.035092922116-0.2221158579050.0315382552375-0.225679419091-0.0534728302460.567012247562-0.06195323359690.3270885561330.02435487987020.04062697324460.276919703595-0.01853971600850.3268469834833.18023545539-33.8607095941-34.2252736932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 280)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 278)

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