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- PDB-3k2l: Crystal Structure of dual-specificity tyrosine phosphorylation re... -

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Basic information

Entry
Database: PDB / ID: 3k2l
TitleCrystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2)
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 2
KeywordsTRANSFERASE / DYRK2 / dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2 / PSK-H2 / kinase / Structural Genomics Consortium / SGC / Apoptosis / ATP-binding / Magnesium / Manganese / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / Tyrosine-protein kinase
Function / homology
Function and homology information


dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of glycogen biosynthetic process / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity ...dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of glycogen biosynthetic process / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity / Regulation of TP53 Activity through Phosphorylation / cytoskeleton / ribonucleoprotein complex / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DYRK / Dual specificity tyrosine-phosphorylation-regulated kinase / Trypsin Inhibitor V; Chain A / 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 ...DYRK / Dual specificity tyrosine-phosphorylation-regulated kinase / Trypsin Inhibitor V; Chain A / 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
Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å
AuthorsFilippakopoulos, P. / Myrianthopoulos, V. / Soundararajan, M. / Krojer, T. / Hapka, E. / Fedorov, O. / Berridge, G. / Wang, J. / Shrestha, L. / Pike, A.C.W. ...Filippakopoulos, P. / Myrianthopoulos, V. / Soundararajan, M. / Krojer, T. / Hapka, E. / Fedorov, O. / Berridge, G. / Wang, J. / Shrestha, L. / Pike, A.C.W. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Mikros, E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2013
Title: Structures of Down Syndrome Kinases, DYRKs, Reveal Mechanisms of Kinase Activation and Substrate Recognition.
Authors: Soundararajan, M. / Roos, A.K. / Savitsky, P. / Filippakopoulos, P. / Kettenbach, A.N. / Olsen, J.V. / Gerber, S.A. / Eswaran, J. / Knapp, S. / Elkins, J.M.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity tyrosine-phosphorylation-regulated kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0476
Polymers49,7611
Non-polymers2865
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.285, 84.285, 148.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 2 / DYRK2


Mass: 49760.863 Da / Num. of mol.: 1 / Fragment: UNP residues 146-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q92630, dual-specificity kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.65 Å3/Da / Density % sol: 53.59 % / Mosaicity: 0.3 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.26M (NH4)2SO4, 0.20M Li2SO4, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.36→42.19 Å / Num. all: 22847 / Num. obs: 22801 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 12.2
Reflection shellResolution: 2.36→2.49 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3275 / Rsym value: 0.899 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.54 Å
Translation2.5 Å40.54 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VX3

2vx3


Resolution: 2.36→40.54 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.289 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.795 / SU B: 20.305 / SU ML: 0.218 / SU R Cruickshank DPI: 0.331 / SU Rfree: 0.268 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.331 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1160 5.1 %RANDOM
Rwork0.225 ---
all0.228 22758 --
obs0.228 22694 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.47 Å2 / Biso mean: 35.014 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20 Å2
2--1.53 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.36→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 13 58 3214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213241
X-RAY DIFFRACTIONr_bond_other_d0.0010.022161
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9754405
X-RAY DIFFRACTIONr_angle_other_deg0.91535251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9185404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87423.448145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03415.088514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9081521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02666
X-RAY DIFFRACTIONr_mcbond_it4.19632025
X-RAY DIFFRACTIONr_mcbond_other1.2483822
X-RAY DIFFRACTIONr_mcangle_it6.11653226
X-RAY DIFFRACTIONr_scbond_it10.72481216
X-RAY DIFFRACTIONr_scangle_it12.453111179
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.554 76 -
Rwork0.426 1564 -
all-1640 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.1617-0.09961.15211.50670.15492.6309-0.17660.5143-0.067-0.3973-0.0071-0.0172-0.41280.34430.18370.2636-0.0404-0.07270.07240.00540.115648.025828.307523.9966
23.1105-0.17911.65261.88230.00055.7325-0.2698-0.04410.2816-0.06220.02050.2726-0.4299-0.73630.24930.08420.0885-0.05370.1529-0.0250.082413.026228.931412.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A62 - 230
2X-RAY DIFFRACTION2A231 - 470

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