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- PDB-3fe3: Crystal structure of the kinase MARK3/Par-1: T211A-S215A double mutant -

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Basic information

Entry
Database: PDB / ID: 3fe3
TitleCrystal structure of the kinase MARK3/Par-1: T211A-S215A double mutant
ComponentsMAP/microtubule affinity-regulating kinase 3
KeywordsTRANSFERASE / SERINE/THREONINE PROTEIN KINASE / MARK / PAR-1 / KIN1 / UBA DOMAIN / C-TAK1 / P78 / MARK3 / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


peptidyl-serine autophosphorylation / negative regulation of protein localization to nucleus / tau-protein kinase activity / negative regulation of hippo signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / tau protein binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants ...peptidyl-serine autophosphorylation / negative regulation of protein localization to nucleus / tau-protein kinase activity / negative regulation of hippo signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / tau protein binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / positive regulation of protein binding / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / extracellular exosome / ATP binding / plasma membrane / cytosol / 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
MAP/microtubule affinity-regulating kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsNugoor, C. / Marx, A. / Panneerselvam, S. / Mandelkow, E.-M. / Mandelkow, E.
Citation
Journal: TO BE PUBLISHED
Title: Crystal structure of the kinase MARK3/Par-1: T211A-S215A double mutant
Authors: Nugoor, C. / Marx, A. / Panneerselvam, S. / 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
DepositionNov 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 3
B: MAP/microtubule affinity-regulating kinase 3


Theoretical massNumber of molelcules
Total (without water)75,2392
Polymers75,2392
Non-polymers00
Water7,170398
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-17 kcal/mol
Surface area29550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.520, 95.330, 111.080
Angle α, β, γ (deg.)90.000, 106.390, 90.000
Int Tables number5
Space group name H-MC121
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein MAP/microtubule affinity-regulating kinase 3 / Cdc25C-associated protein kinase 1 / C-TAK1 / cTAK1 / Serine/threonine protein kinase p78 / Ser/Thr ...Cdc25C-associated protein kinase 1 / C-TAK1 / cTAK1 / Serine/threonine protein kinase p78 / Ser/Thr protein kinase PAR-1 / Protein kinase STK10


Mass: 37619.582 Da / Num. of mol.: 2
Fragment: CATALYTIC AND UBIQUITIN-ASSOCIATED DOMAINS, UNP residues 41-367
Mutation: T211A, S215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MARK3 / Plasmid: PET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI
References: UniProt: P27448, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON THE ISOFORM 3 OF DATABASE MARK3_HUMAN. RESIDUES UNP 162-184 ARE MISSING IN ISOFORM 3.

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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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Hepes, 200mM calcium chloride, 15-18% PEG 3350, 5mM DTT , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MX-225 / Detector: CCD / Date: Jul 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→62.3 Å / Num. obs: 75983 / % possible obs: 99.93 % / Redundancy: 4.95 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 20.89
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.51 / Num. unique all: 5590 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefmac_5.4.0073refinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HAK-E (52-304)

2hak


Resolution: 1.9→51.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.216 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.944 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3856 5.1 %RANDOM
Rwork0.197 ---
obs0.199 75930 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.6 Å2 / Biso mean: 38.066 Å2 / Biso min: 20.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.12 Å2
2---0.12 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→51.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 0 398 5534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225306
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.987146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15923.76250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.747151034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7451542
X-RAY DIFFRACTIONr_chiral_restr0.1470.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213950
X-RAY DIFFRACTIONr_mcbond_it1.2681.53181
X-RAY DIFFRACTIONr_mcangle_it2.09825149
X-RAY DIFFRACTIONr_scbond_it3.25232125
X-RAY DIFFRACTIONr_scangle_it5.114.51992
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9490.3632650.3245319559899.75
1.949-2.0030.3292760.2635153543599.89
2.003-2.0610.2472900.2355045534099.906
2.061-2.1240.2542580.2074884514699.922
2.124-2.1940.2272370.2084740498199.92
2.194-2.270.2562570.2024594485499.938
2.27-2.3560.2642340.20244294663100
2.356-2.4520.2691990.20142724471100
2.452-2.5610.2552450.2144056430399.954
2.561-2.6860.2611930.2013928412299.976
2.686-2.8310.2682200.21337193939100
2.831-3.0020.2262040.21135033707100
3.002-3.2090.2481860.20733163502100
3.209-3.4650.2061680.1933074324399.969
3.465-3.7950.2091370.18928713008100
3.795-4.2410.2011380.16425862724100
4.241-4.8930.1921180.15222822400100
4.893-5.9830.2241140.18719202034100
5.983-8.4230.224800.21715271607100
8.423-62.2570.246370.20585690598.674
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)
13.5550.25762.41513.25491.82114.5192-0.33280.29290.3407-0.41480.3295-0.2351-0.37530.19520.00320.0878-0.08910.0270.1067-0.0164-0.1069-16.888-28.59-44.475
22.22640.44230.61711.17730.34172.02060.13050.0068-0.14460.0076-0.036-0.00870.2923-0.1363-0.09460.00540.0624-0.0170.03860.0182-0.1314-8.151-28.633-19.205
35.95993.2665-1.81653.67381.10668.5459-0.0850.4979-1.00470.09550.5507-0.61981.26370.1803-0.46580.1987-0.0484-0.02120.1334-0.17450.0279-19.979-46.477-50.267
46.5472-1.4806-0.68671.59480.70251.9951-0.2046-0.6521-0.770.16050.12650.14180.08260.10770.078-0.06640.09330.0386-0.03750.0784-0.077-22.9276.439-11.907
52.3627-0.9374-0.15691.7352-0.11942.40210.06610.06910.2159-0.0958-0.0638-0.1359-0.0970.3886-0.0024-0.0862-0.0160.03150.06040.0519-0.1388-1.2694-27.183
64.4283-1.4106-0.85074.48881.31676.82930.1131-0.94740.70410.11890.0054-0.4193-0.43530.5318-0.1184-0.05340.01390.03780.0655-0.1403-0.1094-24.75124.24-4.925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 132
2X-RAY DIFFRACTION2A137 - 316
3X-RAY DIFFRACTION3A331 - 364
4X-RAY DIFFRACTION4B55 - 132
5X-RAY DIFFRACTION5B137 - 316
6X-RAY DIFFRACTION6B331 - 364

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