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- PDB-1kwp: Crystal Structure of MAPKAP2 -

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Basic information

Entry
Database: PDB / ID: 1kwp
TitleCrystal Structure of MAPKAP2
ComponentsMAP Kinase Activated Protein Kinase 2
KeywordsTRANSFERASE / MAPKAP2 / protein kinase / signal transduction
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / macropinocytosis / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / 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 / CREB phosphorylation / macropinocytosis / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / 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 / response to cytokine / regulation of mRNA stability / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / ciliary basal body / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / centrosome / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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
: / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMeng, W. / Swenson, L.L. / Fitzgibbon, M.J. / Hayakawa, K. / ter Haar, E. / Behrens, A.E. / Fulghum, J.R. / Lippke, J.A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of Mitogen-activated Protein Kinase-activated Protein (MAPKAP) Kinase 2 Suggests a Bifunctional Switch That Couples Kinase Activation with Nuclear Export
Authors: Meng, W. / Swenson, L.L. / Fitzgibbon, M.J. / Hayakawa, K. / Ter Haar, E. / Behrens, A.E. / Fulghum, J.R. / Lippke, J.A.
History
DepositionJan 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 4, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.5Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: MAP Kinase Activated Protein Kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,06816
Polymers91,2592
Non-polymers2,80814
Water2,414134
1
A: MAP Kinase Activated Protein Kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0348
Polymers45,6301
Non-polymers1,4047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0348
Polymers45,6301
Non-polymers1,4047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: MAP Kinase Activated Protein Kinase 2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules

A: MAP Kinase Activated Protein Kinase 2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules

A: MAP Kinase Activated Protein Kinase 2
B: MAP Kinase Activated Protein Kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,20348
Polymers273,7786
Non-polymers8,42542
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area28790 Å2
ΔGint-1077 kcal/mol
Surface area79900 Å2
MethodPQS
Unit cell
Length a, b, c (Å)143.944, 143.944, 90.273
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

21A-468-

HOH

31B-476-

HOH

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Components

#1: Protein MAP Kinase Activated Protein Kinase 2 / MAPKAP2


Mass: 45629.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P49137, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.15
Details: 2 M Na/K phosphate, pH 5.15, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris1droppH7.8
2200 mM1dropNaCl
32 mMdithiothreitol1drop
45-10 mg/mlprotein1drop
52 Msodium potassium phospahte1reservoirpH5.15

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→32.6 Å / Num. all: 34168 / Num. obs: 34168 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 11.3 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 4.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.9 / Num. unique all: 2532 / Rsym value: 0.302 / % possible all: 100
Reflection
*PLUS
Num. obs: 17189 / % possible obs: 100 % / Num. measured all: 386514 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Rmerge(I) obs: 0.302

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNXrefinement
REFMACrefinement
CCP4(SCALA)data scaling
CNXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→32.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1702 -RANDOM
Rwork0.233 ---
all0.233 34168 --
obs0.233 34168 100 %-
Refinement stepCycle: LAST / Resolution: 2.8→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 14 134 4899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg3.2
Software
*PLUS
Name: 'CNX AND REFMAC' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.233 / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS

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