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- PDB-1zmv: Catalytic and ubiqutin-associated domains of MARK2/PAR-1: K82R mutant -

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Basic information

Entry
Database: PDB / ID: 1zmv
TitleCatalytic and ubiqutin-associated domains of MARK2/PAR-1: K82R mutant
ComponentsMAP/Microtubule affinity regulating kinase 2
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 / Resolution: 3.105 Å
AuthorsPanneerselvam, S. / Marx, A. / Mandelkow, E.-M. / Mandelkow, E.
CitationJournal: 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.
History
DepositionMay 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: MAP/Microtubule affinity regulating kinase 2
B: MAP/Microtubule affinity regulating kinase 2


Theoretical massNumber of molelcules
Total (without water)75,3512
Polymers75,3512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.191, 121.191, 99.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
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: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTYRTYRAA53 - 13116 - 94
21TYRTYRTYRTYRBB53 - 13116 - 94
12GLYGLYLYSLYSAA135 - 31498 - 277
22GLYGLYLYSLYSBB135 - 31498 - 277
13TYRTYRTYRTYRAA323 - 363286 - 326
23TYRTYRTYRTYRBB323 - 363286 - 326

NCS ensembles :
ID
1
2
3

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Components

#1: Protein MAP/Microtubule affinity regulating kinase 2 / E.C.2.7.1.37 / PAR-1 / Kin1 / serine/threonine kinase Emk / serine/threonine-protein kinase MARK2 / ELKL Motif Kinase / EMK1


Mass: 37675.445 Da / Num. of mol.: 2 / Fragment: CATALYTIC AND UBIQUITIN-ASSOCIATED DOMAINS / Mutation: K82R
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, EC: 2.7.1.37

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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: 2.82 Å3/Da / Density % sol: 56 %
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: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8043 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8043 Å / Relative weight: 1
ReflectionResolution: 3.105→51.78 Å / Num. all: 14813 / Num. obs: 14813 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.109 / Net I/σ(I): 14
Reflection shellResolution: 3.105→3.15 Å / Mean I/σ(I) obs: 2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y8G

1y8g


Resolution: 3.105→51.78 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 41.137 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.153 / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25108 740 5 %RANDOM
Rwork0.19983 ---
all0.20235 14814 --
obs0.20235 14814 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å20 Å2
2--0.35 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 3.105→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4667 0 0 0 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224755
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.9816421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.575583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2123.768207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.51615865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3981532
X-RAY DIFFRACTIONr_chiral_restr0.1140.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023514
X-RAY DIFFRACTIONr_nbd_refined0.2690.22370
X-RAY DIFFRACTIONr_nbtor_refined0.3420.23319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3950.26
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Ens-IDNumberRms dev position (Å)
16140.07
212740.06
33410.09
LS refinement shellResolution: 3.105→3.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 52 -
Rwork0.287 1018 -
obs--96.05 %
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)
14.2252-2.51020.78834.8431-2.47282.16280.0230.57910.2209-0.4431-0.1626-0.2996-0.25260.07430.1396-0.07-0.04880.1556-0.16060.0082-0.206137.412638.266440.2271
23.0365-3.0724-0.00525.101-1.01320.7768-0.0102-0.72580.01920.56380.027-0.2593-0.16290.1043-0.0168-0.0869-0.0318-0.09750.0564-0.1808-0.176746.857526.3554-3.6997
33.2136-0.2845-0.34555.54712.11825.26370.04130.32190.2356-0.23230.00430.2443-0.0385-0.2252-0.0456-0.2367-0.0123-0.0132-0.25860.1256-0.206938.802613.113830.2377
44.6301-0.8058-1.0323.4070.23854.94370.1279-0.2388-0.25940.2257-0.0873-0.03130.20660.1176-0.0406-0.2067-0.0382-0.1393-0.24850.0315-0.185322.777334.25946.0408
518.13892.6437-0.98835.3457-0.661423.10940.0588-1.47260.46260.6297-0.04740.1929-1.49890.6912-0.0114-0.0214-0.06220.1102-0.28510.0929-0.191339.363137.176559.3407
611.29211.0476-1.38643.5458-2.871211.19940.25891.20830.012-0.2164-0.3384-0.30620.21730.09820.0796-0.15030.1751-0.0905-0.0092-0.0748-0.270947.000729.4946-22.5254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA53 - 13116 - 94
2X-RAY DIFFRACTION2BB53 - 13116 - 94
3X-RAY DIFFRACTION3AA135 - 31498 - 277
4X-RAY DIFFRACTION4BB135 - 31498 - 277
5X-RAY DIFFRACTION5AA323 - 363286 - 326
6X-RAY DIFFRACTION6BB323 - 363286 - 326

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