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- PDB-2fys: Crystal structure of Erk2 complex with KIM peptide derived from MKP3 -

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Basic information

Entry
Database: PDB / ID: 2fys
TitleCrystal structure of Erk2 complex with KIM peptide derived from MKP3
Components
  • Dual specificity protein phosphatase 6
  • Mitogen-activated protein kinase 1
KeywordsTRANSFERASE / MAP kinase / MKP3 / KIM
Function / homology
Function and homology information


: / regulation of heart growth / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / : / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation ...: / regulation of heart growth / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / : / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Signaling by Activin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / ESR-mediated signaling / Regulation of the apoptosome activity / Interferon gamma signaling / Signal transduction by L1 / Negative regulation of FGFR2 signaling / response to nitrosative stress / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / FCERI mediated MAPK activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / diadenosine tetraphosphate biosynthetic process / response to xenobiotic stimulus => GO:0009410 / peptidyl-threonine dephosphorylation / Recycling pathway of L1 / neural crest cell development / protein tyrosine/serine/threonine phosphatase activity / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / response to growth factor / mitogen-activated protein kinase kinase kinase binding / regulation of cellular pH / positive regulation of macrophage proliferation / outer ear morphogenesis / Thrombin signalling through proteinase activated receptors (PARs) / RAF/MAP kinase cascade / regulation of Golgi inheritance / mitogen-activated protein kinase binding / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / Neutrophil degranulation / trachea formation / regulation of cytoskeleton organization / regulation of early endosome to late endosome transport / cellular response to organic substance / regulation of stress-activated MAPK cascade / positive regulation of macrophage chemotaxis / response to exogenous dsRNA / lung morphogenesis / protein-serine/threonine phosphatase / ERBB2-ERBB3 signaling pathway / face development / androgen receptor signaling pathway / pseudopodium / progesterone receptor signaling pathway / positive regulation of telomere capping / phosphoprotein phosphatase activity / negative regulation of cell differentiation / Bergmann glial cell differentiation / thyroid gland development / decidualization / steroid hormone mediated signaling pathway / peptidyl-tyrosine dephosphorylation / regulation of ossification / MAP kinase activity / phosphatase binding / mitogen-activated protein kinase / stress-activated MAPK cascade / Schwann cell development / sensory perception of pain
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 / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Mitogen-activated protein (MAP) kinase, ERK1/2 / Rhodanese domain profile. ...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 / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Mitogen-activated protein (MAP) kinase, ERK1/2 / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase 1 / Dual specificity protein phosphatase 6
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, S. / Sun, J.P. / Zhou, B. / Zhang, Z.Y.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis of docking interactions between ERK2 and MAP kinase phosphatase 3
Authors: Liu, S. / Sun, J.P. / Zhou, B. / Zhang, Z.Y.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mitogen-activated protein kinase 1
A: Mitogen-activated protein kinase 1
D: Dual specificity protein phosphatase 6
C: Dual specificity protein phosphatase 6


Theoretical massNumber of molelcules
Total (without water)88,1984
Polymers88,1984
Non-polymers00
Water8,791488
1
B: Mitogen-activated protein kinase 1
D: Dual specificity protein phosphatase 6


Theoretical massNumber of molelcules
Total (without water)44,0992
Polymers44,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-4 kcal/mol
Surface area17170 Å2
MethodPISA
2
A: Mitogen-activated protein kinase 1
C: Dual specificity protein phosphatase 6


Theoretical massNumber of molelcules
Total (without water)44,0992
Polymers44,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.377, 67.478, 86.605
Angle α, β, γ (deg.)90.00, 99.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitogen-activated protein kinase 1 / 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: 42159.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk1, Erk2, Mapk, Prkm1 / Plasmid: NPT7-HIS6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63086, EC: 2.7.1.37
#2: Protein/peptide Dual specificity protein phosphatase 6 / Mitogen-activated protein kinase phosphatase 3 / MAP kinase phosphatase 3 / MKP-3


Mass: 1939.420 Da / Num. of mol.: 2 / Fragment: KIM peptide, residues 60-76 (SWS Q64346) / Source method: obtained synthetically / Details: Chemically synthesized.
References: UniProt: Q64346, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 1.88 Å3/Da / Density % sol: 34.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG3350, 0.1~0.2 M ammonium chloride, 0.1M 2- morpholinoethanesulfonic acid (pH 6.5)., VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 2005
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20430 / % possible obs: 89.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1 / Redundancy: 3.12 % / Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2erk

2erk


Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 551 Random
Rwork0.174 --
obs-20430 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5765 0 0 488 6253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2

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