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- PDB-3brh: Protein Tyrosine Phosphatase PTPN-22 (Lyp) bound to the mono-Phos... -

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Basic information

Entry
Database: PDB / ID: 3brh
TitleProtein Tyrosine Phosphatase PTPN-22 (Lyp) bound to the mono-Phosphorylated Lck active site peptide
Components
  • Lck Active Site Peptide
  • Tyrosine-protein phosphatase non-receptor type 22
KeywordsHYDROLASE / Lyp / PTPN22 / phosphatase / Lck / Alternative splicing / Cytoplasm / Polymorphism / Protein phosphatase / Systemic lupus erythematosus
Function / homology
Function and homology information


phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway ...phosphoanandamide dephosphorylation / positive regulation of granzyme B production / positive regulation of toll-like receptor 3 signaling pathway / regulation of natural killer cell proliferation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of T cell activation / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of interleukin-8 production / negative regulation of JUN kinase activity / negative regulation of T cell receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / regulation of innate immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / phosphatase activity / negative regulation of interleukin-6 production / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of tumor necrosis factor production / T cell differentiation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / protein dephosphorylation / negative regulation of autophagy / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / lipid metabolic process / cytoplasmic side of plasma membrane / autophagy / SH3 domain binding / kinase binding / positive regulation of type II interferon production / T cell receptor signaling pathway / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / negative regulation of gene expression / ubiquitin protein ligase binding / positive regulation of gene expression / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Non-receptor tyrosine-protein phosphatase 22 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...: / Non-receptor tyrosine-protein phosphatase 22 / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsSeidel, R.D. / Love, J. / Piserchio, A. / Cowburn, D.
CitationJournal: To be Published
Title: Lyp/PTPN22 Phosphatase Domain: Substrate Recognition and Specificity for Src family kinases
Authors: Seidel, R. / Love, J. / Piserchio, A. / Cowburn, D.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity_name_com ...database_2 / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / 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 / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 22
B: Tyrosine-protein phosphatase non-receptor type 22
C: Lck Active Site Peptide
D: Lck Active Site Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7196
Polymers74,5294
Non-polymers1902
Water5,296294
1
A: Tyrosine-protein phosphatase non-receptor type 22
C: Lck Active Site Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3603
Polymers37,2652
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-9 kcal/mol
Surface area13870 Å2
MethodPISA
2
B: Tyrosine-protein phosphatase non-receptor type 22
D: Lck Active Site Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3603
Polymers37,2652
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-10 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.850, 48.510, 119.970
Angle α, β, γ (deg.)90.00, 103.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 22 / Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP / PEST-domain ...Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP / PEST-domain phosphatase / PEP


Mass: 36395.695 Da / Num. of mol.: 2 / Fragment: Substrate Trapped Catalytic Domain / Mutation: D195A, C227S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN22, PTPN8 / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase
#2: Protein/peptide Lck Active Site Peptide


Mass: 868.869 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Home sapiens(human).
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAUTHOR STATES THAT RESIDUE 394 IN CHAIN C AND D WAS PTR BUT THE ENZYME CLEAVED IT INTO TYR AND PO4

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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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Bicine, 20% PEG6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9786 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 27, 2007
Details: Bent single Si (111) crystal monochromator with vertical focusing mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 35709 / Num. obs: 34892 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Net I/σ(I): 7.8
Reflection shellResolution: 2.2→2.259 Å / Num. unique all: 2334 / % possible all: 97.46

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
SHARPphasing
RefinementResolution: 2.2→29.591 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1729 -RANDOM
Rwork0.1875 ---
obs0.191 32679 98.596 %-
all-34402 --
Displacement parametersBiso mean: 27.909 Å2
Baniso -1Baniso -2Baniso -3
1-0.003 Å20.005 Å2-0.01 Å2
2--0 Å2-0.004 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 10 295 5335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.022
X-RAY DIFFRACTIONr_angle_refined_deg1.965
LS refinement shellResolution: 2.2→29.6 Å / Rfactor Rfree error: 0.143
RfactorNum. reflection% reflection
Rfree0.26 1703 -
Rwork0.184 --
obs-34402 98.3 %

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