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- PDB-6apx: Crystal structure of human dual specificity phosphatase 1 catalyt... -

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Basic information

Entry
Database: PDB / ID: 6apx
TitleCrystal structure of human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the monobody YSX1
Components
  • Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
  • Monobody YSX1
KeywordsHYDROLASE / Dual specificity phosphatase / DUSP / C258S
Function / homology
Function and homology information


negative regulation of meiotic cell cycle / negative regulation of monocyte chemotaxis / endoderm formation / peptidyl-serine dephosphorylation / negative regulation of DNA biosynthetic process / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-threonine dephosphorylation / negative regulation of p38MAPK cascade ...negative regulation of meiotic cell cycle / negative regulation of monocyte chemotaxis / endoderm formation / peptidyl-serine dephosphorylation / negative regulation of DNA biosynthetic process / MAP kinase tyrosine/serine/threonine phosphatase activity / protein tyrosine/serine/threonine phosphatase activity / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-threonine dephosphorylation / negative regulation of p38MAPK cascade / RAF-independent MAPK1/3 activation / cellular response to chemokine / negative regulation of cell adhesion / mitogen-activated protein kinase binding / growth factor binding / protein-serine/threonine phosphatase / response to testosterone / detection of maltose stimulus / maltose transport complex / negative regulation of MAP kinase activity / protein serine/threonine phosphatase activity / carbohydrate transport / peptidyl-tyrosine dephosphorylation / response to light stimulus / phosphoprotein phosphatase activity / carbohydrate transmembrane transporter activity / response to cAMP / maltose binding / maltose transport / maltodextrin transmembrane transport / response to retinoic acid / cellular response to hormone stimulus / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of MAPK cascade / protein-tyrosine-phosphatase / ATP-binding cassette (ABC) transporter complex / protein tyrosine phosphatase activity / response to glucocorticoid / cell chemotaxis / response to hydrogen peroxide / response to calcium ion / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / response to estradiol / outer membrane-bounded periplasmic space / periplasmic space / intracellular signal transduction / positive regulation of apoptotic process / negative regulation of cell population proliferation / DNA damage response / negative regulation of apoptotic process / signal transduction / nucleus / membrane / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Bacterial extracellular solute-binding protein / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Bacterial extracellular solute-binding protein / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Dual specificity protein phosphatase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.491 Å
AuthorsGumpena, R. / Lountos, G.T. / Sreejith, R.K. / Tropea, J.E. / Cherry, S. / Waugh, D.S.
CitationJournal: Protein Sci. / Year: 2018
Title: Crystal structure of the human dual specificity phosphatase 1 catalytic domain.
Authors: Gumpena, R. / Lountos, G.T. / Raran-Kurussi, S. / Tropea, J.E. / Cherry, S. / Waugh, D.S.
History
DepositionAug 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_mutation
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
B: Monobody YSX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8996
Polymers67,5192
Non-polymers3804
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-73 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.802, 105.802, 181.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1 / MBP / MMBP / Maltodextrin-binding protein / Dual specificity protein phosphatase hVH1 / Mitogen- ...MBP / MMBP / Maltodextrin-binding protein / Dual specificity protein phosphatase hVH1 / Mitogen-activated protein kinase phosphatase 1 / MKP-1 / Protein-tyrosine phosphatase CL100


Mass: 57103.613 Da / Num. of mol.: 1
Mutation: D82A, K83A, E172A, N173A, K239A, K362A, E359A, D363A, C258S
Source method: isolated from a genetically manipulated source
Details: P0AEX9 residues 27-392, P28562-1 residues 172-314
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, DUSP1, CL100, MKP1, PTPN10, VH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEX9, UniProt: P28562, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Protein Monobody YSX1


Mass: 10415.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: 75 mM MES pH 5.9 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 2016
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 36681 / % possible obs: 99.7 % / Redundancy: 17.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 40.1
Reflection shellResolution: 2.49→2.53 Å / Redundancy: 9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2 / Num. unique obs: 1728 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H4Z, 3CSB, 3EZZ

3h4z

3csb

3ezz


Resolution: 2.491→37.268 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1996 5.46 %RANDOM
Rwork0.2068 ---
obs0.2085 36554 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.491→37.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 21 81 4658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084689
X-RAY DIFFRACTIONf_angle_d0.8676399
X-RAY DIFFRACTIONf_dihedral_angle_d7.5722739
X-RAY DIFFRACTIONf_chiral_restr0.052709
X-RAY DIFFRACTIONf_plane_restr0.006827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4915-2.55370.36241330.30122290X-RAY DIFFRACTION94
2.5537-2.62280.36191380.28592420X-RAY DIFFRACTION100
2.6228-2.69990.31231420.25422437X-RAY DIFFRACTION100
2.6999-2.7870.29061410.24652458X-RAY DIFFRACTION100
2.787-2.88660.28921400.23552436X-RAY DIFFRACTION100
2.8866-3.00220.31111410.24692433X-RAY DIFFRACTION100
3.0022-3.13870.28381420.2362466X-RAY DIFFRACTION100
3.1387-3.30410.28581430.22972461X-RAY DIFFRACTION100
3.3041-3.5110.25431420.21632459X-RAY DIFFRACTION100
3.511-3.78180.2421440.19962481X-RAY DIFFRACTION100
3.7818-4.16190.19861420.17832461X-RAY DIFFRACTION99
4.1619-4.76310.19111450.1632503X-RAY DIFFRACTION100
4.7631-5.9970.20981470.19762555X-RAY DIFFRACTION100
5.997-37.27240.20421560.20282698X-RAY DIFFRACTION100

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