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- PDB-1ny3: Crystal structure of ADP bound to MAP KAP kinase 2 -

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Basic information

Entry
Database: PDB / ID: 1ny3
TitleCrystal structure of ADP bound to MAP KAP kinase 2
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE / MAP KAP kinase 2 / MK2 / ADP / kinase / ser/thr kinase
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity ...calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / regulation of interleukin-6 production / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / cellular response to vascular endothelial growth factor stimulus / Regulation of HSF1-mediated heat shock response / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / calmodulin binding / intracellular signal transduction / ciliary basal body / protein phosphorylation / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...MAP kinase activated protein kinase, C-terminal / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ADENOSINE-5'-DIPHOSPHATE / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsUnderwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. ...Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Maguire, M. / Malakian, K. / Telliez, J.B. / Lin, L.L. / Kriz, R.W. / Seehra, J. / Somers, W.S. / Stahl, M.L.
CitationJournal: Structure / Year: 2003
Title: Catalytically active MAP KAP kinase 2 structures in complex with staurosporine and ADP reveal differences with the autoinhibited enzyme
Authors: Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Czerwinski, R.M. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Maguire, M. / Malakian, K. / ...Authors: Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Czerwinski, R.M. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Maguire, M. / Malakian, K. / Telliez, J.B. / Lin, L.L. / Kriz, R.W. / Seehra, J. / Somers, W.S. / Stahl, M.L.
History
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0572
Polymers45,6301
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MAP kinase-activated protein kinase 2
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)552,68324
Polymers547,55712
Non-polymers5,12612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_646-z+3/2,x-1/2,-y+11
crystal symmetry operation11_566y+1/2,-z+1,-x+3/21
crystal symmetry operation27_656-x+3/2,y,-z+3/21
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation36_665-y+1,-z+1,x1
crystal symmetry operation50_655-x+3/2,-y+1/2,z1
crystal symmetry operation54_566z,-x+1,-y+11
crystal symmetry operation58_646-y+1,z-1/2,-x+3/21
crystal symmetry operation76_556x,-y+1/2,-z+3/21
crystal symmetry operation79_665-z+3/2,-x+1,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
Buried area43990 Å2
ΔGint-265 kcal/mol
Surface area145430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)253.049, 253.049, 253.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAPK-2


Mass: 45629.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P49137, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 2.0M Ammonium Sulfate, pH unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMHEPES1reservoirpH7.5
3200 mM1reservoirNaCl
410 mMdithiothreitol1reservoir
55 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2002 / Details: mirrors
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 14402 / Num. obs: 14313 / % possible obs: 99.4 % / Redundancy: 6.96 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 32.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 21 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.29 / Num. unique all: 1385 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 3.1 Å / Num. obs: 12997 / % possible obs: 99.3 % / Num. measured all: 90852 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NZK

1nzk


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.847 / SU B: 14.585 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.624 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29237 674 5 %RANDOM
Rwork0.25913 ---
all0.26981 13470 --
obs0.25913 12796 93.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 86.442 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 27 0 2207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222257
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9713062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9225273
X-RAY DIFFRACTIONr_chiral_restr0.0980.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021661
X-RAY DIFFRACTIONr_nbd_refined0.3190.21197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.25
X-RAY DIFFRACTIONr_mcbond_it10.6491.51383
X-RAY DIFFRACTIONr_mcangle_it14.0722233
X-RAY DIFFRACTIONr_scbond_it22.0533874
X-RAY DIFFRACTIONr_scangle_it28.6484.5829
LS refinement shellResolution: 3.002→3.078 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.39 54
Rwork0.284 784
Refinement
*PLUS
Highest resolution: 3.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.65

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