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- PDB-9bpn: Crystal structure of the allosteric MKP5 mutant Y435W -

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Basic information

Entry
Database: PDB / ID: 9bpn
TitleCrystal structure of the allosteric MKP5 mutant Y435W
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE / MKP5 / Allosteric site mutant
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of epithelial cell migration / negative regulation of p38MAPK cascade / negative regulation of oligodendrocyte differentiation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of epithelial cell migration / negative regulation of p38MAPK cascade / negative regulation of oligodendrocyte differentiation / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / JUN kinase binding / negative regulation of JNK cascade / negative regulation of stress-activated MAPK cascade / positive regulation of regulatory T cell differentiation / dephosphorylation / mitogen-activated protein kinase p38 binding / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of cell migration / negative regulation of ERK1 and ERK2 cascade / negative regulation of epithelial cell proliferation / Negative regulation of MAPK pathway / response to lipopolysaccharide / signal transduction / nucleoplasm / nucleus / cytosol / 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 / 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
Dual specificity protein phosphatase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsManjula, R. / Bennett, A.M. / Lolis, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)RO1 HL158876 United States
CitationJournal: To Be Published
Title: Dynamic and structural insights into allosteric regulation on MKP5/DUSP10 a dual-specificity phosphatase
Authors: Manjula, R. / Bennett, A.M. / Lolis, E.
History
DepositionMay 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity protein phosphatase 10
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)34,1792
Polymers34,1792
Non-polymers00
Water63135
1
A: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0901
Polymers17,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)17,0901
Polymers17,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.862, 44.744, 87.326
Angle α, β, γ (deg.)90.00, 109.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MAP kinase phosphatase 5 / MKP-5


Mass: 17089.617 Da / Num. of mol.: 2 / Mutation: Y435W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8.5, 3 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.96 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.4→28 Å / Num. obs: 14236 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.057 / Rrim(I) all: 0.148 / Χ2: 0.92 / Net I/σ(I): 10.6 / Num. measured all: 96455
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.651 / Num. measured all: 9952 / Num. unique obs: 1494 / CC1/2: 0.892 / Rpim(I) all: 0.272 / Rrim(I) all: 0.707 / Χ2: 0.74 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→28 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2879 699 4.91 %
Rwork0.2255 --
obs0.2287 14229 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 0 35 2292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152311
X-RAY DIFFRACTIONf_angle_d1.4453138
X-RAY DIFFRACTIONf_dihedral_angle_d15.573312
X-RAY DIFFRACTIONf_chiral_restr0.062354
X-RAY DIFFRACTIONf_plane_restr0.01407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.32651490.26282684X-RAY DIFFRACTION100
2.59-2.850.36051350.27092670X-RAY DIFFRACTION100
2.85-3.260.33991350.24822689X-RAY DIFFRACTION100
3.26-4.10.25171370.20652716X-RAY DIFFRACTION100
4.1-280.27051430.21092771X-RAY DIFFRACTION100

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