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- PDB-2r0i: Crystal structure of a kinase MARK2/Par-1 mutant -

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Basic information

Entry
Database: PDB / ID: 2r0i
TitleCrystal structure of a kinase MARK2/Par-1 mutant
ComponentsSerine/threonine-protein kinase MARK2
KeywordsSIGNALING PROTEIN / TRANSFERASE / SERINE/THREONINE PROTEIN KINASE / MARK / PAR-1 / KIN1 / UBA DOMAIN
Function / homology
Function and homology information


establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / basal cortex / regulation of microtubule binding / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of postsynapse organization / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity ...establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / basal cortex / regulation of microtubule binding / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of postsynapse organization / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity / axon development / regulation of cytoskeleton organization / lateral plasma membrane / regulation of microtubule cytoskeleton organization / molecular function activator activity / actin filament / neuron migration / tau protein binding / Wnt signaling pathway / positive regulation of neuron projection development / microtubule cytoskeleton organization / postsynapse / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / lipid binding / dendrite / magnesium ion binding / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...: / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Helicase, Ruva Protein; domain 3 / 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
Serine/threonine-protein kinase MARK2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.202 Å
AuthorsPanneerselvam, S. / Marx, A. / Mandelkow, E.-M. / Mandelkow, E.
Citation
Journal: To be Published
Title: Crystal structure of a kinase MARK2/Par-1 mutant
Authors: Panneerselvam, S. / Marx, A. / Mandelkow, E.-M. / Mandelkow, E.
#1: Journal: Structure / Year: 2006
Title: Structure of the Catalytic and Ubiquitin-Associated Domains of the Protein Kinase MARK/Par-1
Authors: Panneerselvam, S. / Marx, A. / Mandelkow, E.-M. / Mandelkow, E.
#2: Journal: J.Biol.Chem. / Year: 2006
Title: Structural Variations in the Catalytic and Ubiquitin-associated Domains of Microtubule-associated Protein/Microtubule Affinity Regulating Kinase (MARK) 1 and MARK2
Authors: Marx, A. / Nugoor, C. / Muller, J. / Panneerselvam, S. / Timm, T. / Bilang, M. / Mylonas, E. / Svergun, D.I. / Mandelkow, E.-M. / Mandelkow, E.
History
DepositionAug 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase MARK2
B: Serine/threonine-protein kinase MARK2


Theoretical massNumber of molelcules
Total (without water)75,1792
Polymers75,1792
Non-polymers00
Water2,000111
1
A: Serine/threonine-protein kinase MARK2


Theoretical massNumber of molelcules
Total (without water)37,5891
Polymers37,5891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase MARK2


Theoretical massNumber of molelcules
Total (without water)37,5891
Polymers37,5891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.405, 120.405, 99.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLYGLYAA48 - 13411 - 97
21PROPROGLYGLYBB48 - 13411 - 97
12GLYGLYTYRTYRAA135 - 31698 - 279
22GLYGLYTYRTYRBB135 - 31698 - 279
13TYRTYRTYRTYRAA323 - 363286 - 326
23TYRTYRTYRTYRBB323 - 363286 - 326

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Serine/threonine-protein kinase MARK2 / E.C.2.7.11.1 / MAP/microtubule affinity-regulating kinase 2 / ELKL Motif Kinase / EMK1


Mass: 37589.395 Da / Num. of mol.: 2 / Fragment: CATALYTIC AND UBIQUITIN-ASSOCIATED DOMAINS / Mutation: E318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: MARK2 / Plasmid: PDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI
References: UniProt: O08679, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, AMMONIUM SULPHATE, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.2→150 Å / Num. obs: 41338 / % possible obs: 99 % / Rmerge(I) obs: 0.041 / Χ2: 0.728 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.240.54920651.144199.8
2.24-2.280.47520651.108199.7
2.28-2.320.3920861.074199.7
2.32-2.370.3520871.0761100
2.37-2.420.29420551.057199.7
2.42-2.480.25820621.029199.6
2.48-2.540.20920870.989199.6
2.54-2.610.16120770.887199.6
2.61-2.690.14320520.938199.6
2.69-2.770.10820550.83199.1
2.77-2.870.08920800.729199.4
2.87-2.990.07220610.699199.5
2.99-3.120.05820860.64199
3.12-3.290.04820500.587199.3
3.29-3.490.03920580.458198.8
3.49-3.760.03320790.29198.7
3.76-4.140.0320560.296198.5
4.14-4.740.02820750.244198.3
4.74-5.970.02820660.217198.1
5.97-1500.02620360.345194.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZMU

1zmu


Resolution: 2.202→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.194 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2112 5.1 %RANDOM
Rwork0.192 ---
all0.194 ---
obs0.194 41337 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.822 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.202→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4744 0 0 111 4855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224886
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.986603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7115608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44523.684209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02315897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1641531
X-RAY DIFFRACTIONr_chiral_restr0.1290.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023613
X-RAY DIFFRACTIONr_nbd_refined0.2160.22064
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23317
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.214
X-RAY DIFFRACTIONr_mcbond_it1.2131.53109
X-RAY DIFFRACTIONr_mcangle_it1.90224841
X-RAY DIFFRACTIONr_scbond_it3.11132056
X-RAY DIFFRACTIONr_scangle_it4.5984.51757
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1349TIGHT POSITIONAL0.070.05
1331LOOSE POSITIONAL0.35
1349TIGHT THERMAL0.280.5
1331LOOSE THERMAL1.9910
2660TIGHT POSITIONAL0.060.05
2639LOOSE POSITIONAL0.255
2660TIGHT THERMAL0.240.5
2639LOOSE THERMAL1.3910
3164TIGHT POSITIONAL0.110.05
3169LOOSE POSITIONAL0.545
3164TIGHT THERMAL0.330.5
3169LOOSE THERMAL1.7410
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 161 -
Rwork0.231 2886 -
all-3047 -
obs--99.87 %
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)
13.119-0.52670.30713.9797-0.9333.0523-0.06070.45980.03420.1195-0.1918-0.2084-0.28440.15550.2524-0.0453-0.05120.0408-0.0629-0.0136-0.125837.744338.35540.3908
21.4381-0.5802-0.60793.19561.33892.70530.17690.11280.1262-0.1038-0.01710.0639-0.0992-0.0264-0.1598-0.0180.0049-0.0055-0.14910.0328-0.059438.418113.271530.8856
33.90580.34191.10931.9159-0.71611.22550.051-0.3163-0.02630.11420.07420.1567-0.48720.1785-0.1252-0.0360.00990.0941-0.1336-0.0009-0.094439.088737.022959.537
42.4941-0.4988-0.48412.50330.21651.0745-0.0129-0.23280.1220.3041-0.07070.0146-0.1049-0.02020.0836-0.0689-0.00270.0127-0.061-0.0404-0.125846.86227.0095-3.6344
52.7017-0.9536-1.09771.88721.30352.62710.0392-0.0448-0.05580.05920.0339-0.05060.081-0.0175-0.073-0.11210.0326-0.0387-0.11220.0218-0.031122.598834.0095.4151
63.83790.00531.48493.1317-4.20018.35370.03830.3932-0.0298-0.3193-0.101-0.09090.32320.24580.0627-0.04720.05060.031-0.0473-0.0401-0.132746.678430.0825-22.4957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA48 - 13411 - 97
2X-RAY DIFFRACTION2AA135 - 31698 - 279
3X-RAY DIFFRACTION3AA323 - 363286 - 326
4X-RAY DIFFRACTION4BB48 - 13411 - 97
5X-RAY DIFFRACTION5BB135 - 31698 - 279
6X-RAY DIFFRACTION6BB323 - 363286 - 326

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