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- PDB-6rfp: ERK2 MAP kinase with mutations at Helix-G -

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Basic information

Entry
Database: PDB / ID: 6rfp
TitleERK2 MAP kinase with mutations at Helix-G
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / NleD / effectors / T3SS / MAP kinase / phosphorylation
Function / homology
Function and homology information


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 / Transcriptional and post-translational regulation of MITF-M expression and 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 / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / IFNG signaling activates MAPKs / Golgi Cisternae Pericentriolar Stack Reorganization / Estrogen-stimulated signaling through PRKCZ / Regulation of actin dynamics for phagocytic cup formation / 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 / Regulation of the apoptosome activity / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / diadenosine tetraphosphate biosynthetic process / Recycling pathway of L1 / neural crest cell development / response to alcohol / cellular response to toxic substance / cellular response to methionine / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / mitogen-activated protein kinase kinase kinase binding / cytosine metabolic process / response to epidermal growth factor / positive regulation of macrophage proliferation / outer ear morphogenesis / RAF/MAP kinase cascade / regulation of cellular pH / Thrombin signalling through proteinase activated receptors (PARs) / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / Neutrophil degranulation / mammary gland epithelial cell proliferation / trachea formation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / cellular response to insulin-like growth factor stimulus / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / androgen receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / pseudopodium / response to testosterone / positive regulation of telomere capping / Bergmann glial cell differentiation / thyroid gland development / negative regulation of cell differentiation / decidualization / steroid hormone receptor signaling pathway / MAP kinase activity / regulation of ossification / estrous cycle / mitogen-activated protein kinase / phosphatase binding / progesterone receptor signaling pathway / Schwann cell development / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / cellular response to cAMP / positive regulation of telomere maintenance via telomerase / cellular response to epidermal growth factor stimulus / sensory perception of pain / phosphotyrosine residue binding / cellular response to cadmium ion / myelination / ERK1 and ERK2 cascade / cellular response to amino acid starvation
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
Similarity search - Domain/homology
Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLivnah, O. / Eitan-Wexler, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1422/16 Israel
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The bacterial metalloprotease NleD selectively cleaves mitogen-activated protein kinases that have high flexibility in their activation loop.
Authors: Gur-Arie, L. / Eitan-Wexler, M. / Weinberger, N. / Rosenshine, I. / Livnah, O.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2May 27, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 24, 2024Group: 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:
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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)43,4261
Polymers43,4261
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.740, 68.810, 60.810
Angle α, β, γ (deg.)90.00, 110.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitogen-activated protein kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK ...MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAPK 2


Mass: 43425.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk1, Erk2, Mapk, Prkm1 / Production host: Escherichia coli (E. coli)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.8 M ammonium sulfate 0.1 M Bis-tris pH 6.8 or 6.5 2% (w/v) PEG 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.74→45.8 Å / Num. obs: 38438 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rsym value: 0.047 / Net I/σ(I): 16.1
Reflection shellResolution: 1.74→1.79 Å / Num. unique obs: 2840 / Rsym value: 0.661

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S31

4s31


Resolution: 1.74→45.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.377 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19726 1925 5 %RANDOM
Rwork0.14386 ---
obs0.14652 36513 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.781 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20.14 Å2
2---1.07 Å20 Å2
3---1.37 Å2
Refinement stepCycle: 1 / Resolution: 1.74→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2747 0 0 227 2974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132823
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172662
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.6433820
X-RAY DIFFRACTIONr_angle_other_deg1.4951.5786182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34822.403154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58215506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4161518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023082
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9653.3631351
X-RAY DIFFRACTIONr_mcbond_other5.9463.3621350
X-RAY DIFFRACTIONr_mcangle_it6.645.0261680
X-RAY DIFFRACTIONr_mcangle_other6.6455.0271681
X-RAY DIFFRACTIONr_scbond_it7.744.0291472
X-RAY DIFFRACTIONr_scbond_other7.7424.0291470
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9255.8012140
X-RAY DIFFRACTIONr_long_range_B_refined8.60541.3233285
X-RAY DIFFRACTIONr_long_range_B_other8.61641.0983251
X-RAY DIFFRACTIONr_rigid_bond_restr4.68735485
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.742→1.788 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 172 -
Rwork0.224 2659 -
obs--99.47 %

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