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- PDB-2wzj: Catalytic and UBA domain of kinase MARK2/(Par-1) K82R, T208E doub... -

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Basic information

Entry
Database: PDB / ID: 2wzj
TitleCatalytic and UBA domain of kinase MARK2/(Par-1) K82R, T208E double mutant
ComponentsSERINE/THREONINE-PROTEIN KINASE MARK2
KeywordsTRANSFERASE / UBA DOMAIN / SERINE/THREONINE-PROTEIN KINASE / SIGNALING PROTEIN / S/T PROTEIN KINASE / DIFFERENTIATION / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


microtubule bundle / establishment or maintenance of cell polarity regulating cell shape / basal cortex / regulation of neurofibrillary tangle assembly / establishment or maintenance of epithelial cell apical/basal polarity / tau-protein kinase / regulation of postsynapse organization / tau-protein kinase activity / regulation of axonogenesis / regulation of cytoskeleton organization ...microtubule bundle / establishment or maintenance of cell polarity regulating cell shape / basal cortex / regulation of neurofibrillary tangle assembly / establishment or maintenance of epithelial cell apical/basal polarity / tau-protein kinase / regulation of postsynapse organization / tau-protein kinase activity / regulation of axonogenesis / regulation of cytoskeleton organization / axon development / establishment of cell polarity / lateral plasma membrane / regulation of microtubule cytoskeleton organization / actin filament / positive regulation of neuron projection development / peptidyl-serine phosphorylation / microtubule cytoskeleton organization / tau protein binding / Wnt signaling pathway / neuron migration / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / postsynapse / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / lipid binding / glutamatergic synapse / magnesium ion binding / ATP binding / nucleus / membrane / 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 / 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
Serine/threonine-protein kinase MARK2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.786 Å
AuthorsPanneerselvam, S. / Marx, A. / Mandelkow, E.-M. / Mandelkow, E.
Citation
Journal: Faseb J. / Year: 2010
Title: Structure and Function of Polarity-Inducing Kinase Family Mark/Par-1 within the Branch of Ampk/Snf1-Related Kinases.
Authors: Marx, A. / Nugoor, C. / Panneerselvam, S. / 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. / 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. / Mandelkow, E.
History
DepositionNov 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE MARK2
B: SERINE/THREONINE-PROTEIN KINASE MARK2
C: SERINE/THREONINE-PROTEIN KINASE MARK2
D: SERINE/THREONINE-PROTEIN KINASE MARK2
E: SERINE/THREONINE-PROTEIN KINASE MARK2
F: SERINE/THREONINE-PROTEIN KINASE MARK2


Theoretical massNumber of molelcules
Total (without water)226,2216
Polymers226,2216
Non-polymers00
Water2,072115
1
D: SERINE/THREONINE-PROTEIN KINASE MARK2
E: SERINE/THREONINE-PROTEIN KINASE MARK2


Theoretical massNumber of molelcules
Total (without water)75,4072
Polymers75,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-24.7 kcal/mol
Surface area28600 Å2
MethodPISA
2
A: SERINE/THREONINE-PROTEIN KINASE MARK2
F: SERINE/THREONINE-PROTEIN KINASE MARK2


Theoretical massNumber of molelcules
Total (without water)75,4072
Polymers75,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-24.4 kcal/mol
Surface area28290 Å2
MethodPISA
3
B: SERINE/THREONINE-PROTEIN KINASE MARK2
C: SERINE/THREONINE-PROTEIN KINASE MARK2


Theoretical massNumber of molelcules
Total (without water)75,4072
Polymers75,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-25.9 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.240, 205.578, 91.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
SERINE/THREONINE-PROTEIN KINASE MARK2 / MAP/MICROTUBULE AFFINITY-REGULATING KINASE 2 / ELKL MOTIF KINASE / EMK1 / MARK2


Mass: 37703.453 Da / Num. of mol.: 6 / Fragment: CATALYTIC AND UBA DOMAINS, RESIDUES 39-364 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / 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.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 82 TO ARG ENGINEERED RESIDUE IN CHAIN A, THR 208 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, LYS 82 TO ARG ENGINEERED RESIDUE IN CHAIN A, THR 208 TO GLU ENGINEERED RESIDUE IN CHAIN B, LYS 82 TO ARG ENGINEERED RESIDUE IN CHAIN B, THR 208 TO GLU ENGINEERED RESIDUE IN CHAIN C, LYS 82 TO ARG ENGINEERED RESIDUE IN CHAIN C, THR 208 TO GLU ENGINEERED RESIDUE IN CHAIN D, LYS 82 TO ARG ENGINEERED RESIDUE IN CHAIN D, THR 208 TO GLU ENGINEERED RESIDUE IN CHAIN E, LYS 82 TO ARG ENGINEERED RESIDUE IN CHAIN E, THR 208 TO GLU ENGINEERED RESIDUE IN CHAIN F, LYS 82 TO ARG ENGINEERED RESIDUE IN CHAIN F, THR 208 TO GLU
Has protein modificationY
Sequence detailsG38 EXPRESSION TAG, R82 AND E208 ENGINEERED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.46 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 60% TACSIMATE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 76705 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.97 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.64
Reflection shellResolution: 2.78→2.95 Å / Redundancy: 4.94 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.49 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZMU

1zmu


Resolution: 2.786→45.394 Å / SU ML: 0.43 / σ(F): 2 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 3850 5 %
Rwork0.1786 --
obs0.1819 76630 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.083 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.8005 Å20 Å20 Å2
2--9.0959 Å20 Å2
3---2.7046 Å2
Refinement stepCycle: LAST / Resolution: 2.786→45.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15211 0 0 115 15326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815521
X-RAY DIFFRACTIONf_angle_d1.13820892
X-RAY DIFFRACTIONf_dihedral_angle_d18.2755868
X-RAY DIFFRACTIONf_chiral_restr0.0782283
X-RAY DIFFRACTIONf_plane_restr0.0042664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7855-2.82080.36081560.27852455X-RAY DIFFRACTION93
2.8208-2.85790.3541480.26582688X-RAY DIFFRACTION100
2.8579-2.8970.35691510.25682626X-RAY DIFFRACTION100
2.897-2.93840.34091370.26182681X-RAY DIFFRACTION100
2.9384-2.98220.34781290.23632663X-RAY DIFFRACTION100
2.9822-3.02880.29181230.2342704X-RAY DIFFRACTION100
3.0288-3.07850.3021440.22272660X-RAY DIFFRACTION100
3.0785-3.13160.29161260.21162684X-RAY DIFFRACTION100
3.1316-3.18850.29061370.212674X-RAY DIFFRACTION100
3.1885-3.24980.30311430.2052702X-RAY DIFFRACTION100
3.2498-3.31610.27791270.18952683X-RAY DIFFRACTION100
3.3161-3.38820.27151330.18682687X-RAY DIFFRACTION100
3.3882-3.4670.25751500.19082665X-RAY DIFFRACTION100
3.467-3.55360.25121460.1772664X-RAY DIFFRACTION100
3.5536-3.64970.30711510.18122718X-RAY DIFFRACTION100
3.6497-3.7570.25481420.17222661X-RAY DIFFRACTION100
3.757-3.87820.21771610.15352697X-RAY DIFFRACTION100
3.8782-4.01680.25231250.1492704X-RAY DIFFRACTION100
4.0168-4.17750.20361490.13962695X-RAY DIFFRACTION100
4.1775-4.36750.191440.13642716X-RAY DIFFRACTION100
4.3675-4.59750.20061370.13282709X-RAY DIFFRACTION100
4.5975-4.88530.20561370.13182731X-RAY DIFFRACTION100
4.8853-5.26190.19161540.13162724X-RAY DIFFRACTION100
5.2619-5.79050.20421300.15072752X-RAY DIFFRACTION100
5.7905-6.62620.22711390.1612777X-RAY DIFFRACTION100
6.6262-8.33990.20971650.15812771X-RAY DIFFRACTION100
8.3399-45.40020.21451660.17782889X-RAY DIFFRACTION99
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)
11.0185-0.18630.40770.3465-0.27420.60290.0716-0.1321-0.16060.0179-0.053-0.0052-0.0460.1741-00.24770.00540.01660.28190.04150.15459.1749-55.4274-38.1756
21.2354-0.13580.18350.36380.19560.49410.10160.08920.03650.03-0.1158-0.10580.10120.122200.25480.0152-0.02470.21280.01080.10883.6768-36.705-66.3995
31.4645-0.36750.32660.74870.05680.51580.0629-0.2240.07890.0748-0.09540.37030.08120.01020.00030.1764-0.05150.14190.1224-0.06330.2851-32.4948-30.4213-68.0286
40.3377-0.43390.00290.11340.05950.78820.21390.01510.2943-0.0076-0.0944-0.1433-0.0632-0.0094-00.1919-0.03280.06510.2526-0.05120.2601-45.2894-45.7724-96.475
50.57570.1503-0.38350.70390.1730.8020.2005-0.2647-0.33150.2461-0.1725-0.16930.1957-0.02080.01990.3525-0.1042-0.13260.28060.22190.532-33.4641-80.1323-99.8712
61.53130.73530.28280.94650.13390.6173-0.19940.2555-0.9618-0.26830.3976-0.15190.0421-0.04910.04330.2904-0.0645-0.00150.109-0.0640.9013-15.012-82.7229-37.9624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

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