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- PDB-3d42: Crystal structure of HePTP in complex with a monophosphorylated E... -

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Basic information

Entry
Database: PDB / ID: 3d42
TitleCrystal structure of HePTP in complex with a monophosphorylated Erk2 peptide
Components
  • Mitogen-activated protein kinase 1 peptide
  • Tyrosine-protein phosphatase non-receptor type 7
KeywordsHYDROLASE / HEPTP / HUMAN HEMATOPOIETIC TYROSINE PHOSPHATASE CATALYTIC DOMAIN MUTANT / LC-PTP / PTPN7 / ERK2 / PTP-PEPTIDE COMPLEX / MAPK-DERIVED PEPTIDE / Phosphoprotein / Protein phosphatase / ATP-binding / Cell cycle / Host-virus interaction / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Transferase
Function / homology
Function and homology information


phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process ...phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / Signaling by NODAL / ERKs are inactivated / Signaling by MAP2K mutants / RSK activation / Interleukin-37 signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of the apoptosome activity / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / Signaling by LTK in cancer / regulation of Golgi inheritance / positive regulation of peptidyl-threonine phosphorylation / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / IFNG signaling activates MAPKs / regulation of stress-activated MAPK cascade / Frs2-mediated activation / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / response to exogenous dsRNA / MAPK1 (ERK2) activation / pseudopodium / lung morphogenesis / face development / positive regulation of telomere maintenance / Bergmann glial cell differentiation / Recycling pathway of L1 / non-membrane spanning protein tyrosine phosphatase activity / thyroid gland development / Advanced glycosylation endproduct receptor signaling / peptidyl-threonine phosphorylation / MAP kinase activity / regulation of ossification / negative regulation of cell differentiation / Regulation of HSF1-mediated heat shock response / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mitogen-activated protein kinase / RHO GTPases Activate WASPs and WAVEs / Signal attenuation / phosphatase binding / Growth hormone receptor signaling / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / protein dephosphorylation / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / phosphotyrosine residue binding / myelination / protein-tyrosine-phosphatase / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / protein tyrosine phosphatase activity / ESR-mediated signaling / lipopolysaccharide-mediated signaling pathway / cellular response to amino acid starvation / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / B cell receptor signaling pathway / response to nicotine / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of cholesterol biosynthetic process / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Oncogene Induced Senescence / caveola / regulation of protein stability
Similarity search - Function
Protein-tyrosine phosphatase, KIM-containing / Mitogen-activated protein (MAP) kinase, ERK1/2 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase ...Protein-tyrosine phosphatase, KIM-containing / Mitogen-activated protein (MAP) kinase, ERK1/2 / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Mitogen-activated protein kinase 1 / Tyrosine-protein phosphatase non-receptor type 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsCritton, D.A. / Tortajada, A. / Page, R.
CitationJournal: Biochemistry / Year: 2008
Title: Structural basis of substrate recognition by hematopoietic tyrosine phosphatase.
Authors: Critton, D.A. / Tortajada, A. / Stetson, G. / Peti, W. / Page, R.
History
DepositionMay 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 7
B: Mitogen-activated protein kinase 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4784
Polymers36,2362
Non-polymers2422
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.460, 39.035, 83.650
Angle α, β, γ (deg.)90.00, 124.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 7 / Protein-tyrosine phosphatase LC-PTP / Hematopoietic protein-tyrosine phosphatase / HEPTP


Mass: 35202.711 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 65-360) / Mutation: T106D, C270S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN7 / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P35236, protein-tyrosine-phosphatase
#2: Protein/peptide Mitogen-activated protein kinase 1 peptide / Extracellular signal-regulated kinase 2 / ERK-2 / Mitogen-activated protein kinase 2 / MAP kinase 2 ...Extracellular signal-regulated kinase 2 / ERK-2 / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2 / p42-MAPK / ERT1


Mass: 1033.050 Da / Num. of mol.: 1 / Fragment: Activation loop (UNP residues 184-191) / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS / References: UniProt: P28482
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2 M AMMONIUM TARTRATE DIBASIC, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 29, 2008
Details: SI(III) CHANNEL CUT MONOCHROMATOR, OXFORD DANFYSIK TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(III) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 11129 / Num. obs: 10896 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.111
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.221 / Num. unique all: 1048 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QDM

2qdm


Resolution: 2.46→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.88 / SU B: 7.943 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.813 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24082 524 4.7 %RANDOM
Rwork0.1813 ---
all0.216 10831 --
obs0.18414 10585 94.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20.32 Å2
2--0.17 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.46→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 16 122 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222384
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9663246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22323.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80215379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6991517
X-RAY DIFFRACTIONr_chiral_restr0.3820.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021835
X-RAY DIFFRACTIONr_nbd_refined0.2130.21107
X-RAY DIFFRACTIONr_nbtor_refined0.310.21588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.216
X-RAY DIFFRACTIONr_mcbond_it2.28331514
X-RAY DIFFRACTIONr_mcangle_it3.26852370
X-RAY DIFFRACTIONr_scbond_it4.98681002
X-RAY DIFFRACTIONr_scangle_it6.63711876
LS refinement shellResolution: 2.455→2.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 37 -
Rwork0.199 711 -
obs--88.21 %

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