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- PDB-2vx3: Crystal structure of the human dual specificity tyrosine- phospho... -

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Basic information

Entry
Database: PDB / ID: 2vx3
TitleCrystal structure of the human dual specificity tyrosine- phosphorylation-regulated kinase 1A
ComponentsDUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / MINIBRAIN HOMOLOG / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / TYROSINE-PROTEIN KINASE / CASP8 / KINASE
Function / homology
Function and homology information


histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / tau protein binding / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / 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 ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / 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
Chem-D15 / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRoos, A.K. / Soundararajan, M. / Pike, A.C.W. / Federov, O. / King, O. / Burgess-Brown, N. / Philips, C. / Filippakopoulos, P. / Arrowsmith, C.H. / Wikstrom, M. ...Roos, A.K. / Soundararajan, M. / Pike, A.C.W. / Federov, O. / King, O. / Burgess-Brown, N. / Philips, C. / Filippakopoulos, P. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A. / von Delft, F. / Bountra, C. / Knapp, S.
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
DepositionJun 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Jun 26, 2013Group: Database references / Derived calculations
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
B: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
C: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
D: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,31532
Polymers178,2134
Non-polymers5,10228
Water3,693205
1
A: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9807
Polymers44,5531
Non-polymers1,4266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,20710
Polymers44,5531
Non-polymers1,6549
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6438
Polymers44,5531
Non-polymers1,0897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4867
Polymers44,5531
Non-polymers9336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)264.203, 65.105, 140.282
Angle α, β, γ (deg.)90.00, 115.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A136 - 212
2115B136 - 212
3115C136 - 212
4115D136 - 212
1214A220 - 406
2214B220 - 406
3214C220 - 406
4214D220 - 406
1314A413 - 480
2314B413 - 480
3314C413 - 480
4314D413 - 480

NCS oper:
IDCodeMatrixVector
1given(-0.603, -0.797, -0.028), (-0.796, 0.599, 0.084), (-0.05, 0.073, -0.996)22.05035, 15.78841, -104.34769
2given(0.843, 0.482, -0.238), (0.473, -0.875, -0.1), (-0.256, -0.029, -0.966)-20.29074, -10.69172, -41.35233
3given(0.885, -0.404, -0.23), (-0.391, -0.915, 0.102), (-0.252, -0.968)-63.48191, 28.85044, -65.01735

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A / PROTEIN KINASE MINIBRAIN HOMOLOG / MNBH / HMNB / HP86 / DUAL SPECIFICITY YAK1-RELATED KINASE


Mass: 44553.188 Da / Num. of mol.: 4 / Fragment: RESIDUES 127-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q13627, dual-specificity kinase

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Non-polymers , 5 types, 233 molecules

#2: Chemical
ChemComp-D15 / N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}-1H-indazol-3-yl)benzamide


Mass: 447.917 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H22ClN5O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPHOSPHOTYROSINE (PTR): PHOSPHORYLATED TYROSINE

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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: 3.02 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 8.5 / Details: 34% PEG 300, 0.1 M LISO4, TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: May 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→26.35 Å / Num. obs: 92815 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EXE AND 1Z57

1exe

1z57


Resolution: 2.4→26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.127 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1799 2.1 %RANDOM
Rwork0.185 ---
obs0.186 82846 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-1.13 Å2
2--0.4 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11050 0 280 205 11535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211620
X-RAY DIFFRACTIONr_bond_other_d0.0010.028055
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.98615676
X-RAY DIFFRACTIONr_angle_other_deg0.9193.00219456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86751367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90123.569538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.738151996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2851575
X-RAY DIFFRACTIONr_chiral_restr0.0910.21652
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022400
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.78136822
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.988510974
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.64384798
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.017114699
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3780medium positional0.220.5
2B3780medium positional0.280.5
3C3780medium positional0.220.5
4D3780medium positional0.20.5
1A596loose positional0.355
2B596loose positional0.315
3C596loose positional0.335
4D596loose positional0.365
1A3780medium thermal1.092
2B3780medium thermal0.992
3C3780medium thermal0.872
4D3780medium thermal0.892
1A596loose thermal0.910
2B596loose thermal0.9610
3C596loose thermal0.8810
4D596loose thermal1.0210
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 138
Rwork0.34 6015
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)
13.3682-0.51590.5363.80090.45142.6374-0.0031-0.2004-0.08760.22060.0447-0.33360.00720.1444-0.04170.2484-0.0172-0.06480.07-0.05230.070942.2129.3901-30.5632
21.14190.01380.221.2875-0.08941.42630.0767-0.07860.00690.1602-0.0190.0019-0.1034-0.0682-0.05760.1047-0.0158-0.0008-0.05240.02520.045425.323520.1484-46.8043
35.1437-2.5307-3.49875.66291.86294.64620.43740.87920.14-0.7925-0.26140.2857-0.6857-0.774-0.17610.19070.0422-0.07130.19060.08050.019112.725528.2429-69.555
41.8881-0.32120.22141.70160.00361.77910.0316-0.0805-0.26460.1528-0.00860.11250.1541-0.0347-0.0229-0.0061-0.035-0.0216-0.04880.02830.10419.73727.5585-52.0806
52.41650.67380.80075.004-0.63632.49260.0298-0.0094-0.3099-0.1337-0.02060.09340.0811-0.0359-0.00930.06110.0576-0.07330.2892-0.03510.1067-26.9832-3.043-72.9511
63.15040.31431.3220.7461-0.20631.45430.11870.1997-0.1383-0.0578-0.088-0.0154-0.0263-0.0568-0.03060.03350.01870.03110.2012-0.01220.0866-11.7401-1.4935-67.1036
72.2182-0.1776-0.10062.14370.37831.25060.1292-0.35060.02240.4285-0.0669-0.06-0.0083-0.1712-0.06240.0909-0.06890.01380.19530.02910.0952-4.43087.5777-47.2344
83.31990.05490.92150.86810.01471.48180.11340.2314-0.192-0.15790.0525-0.22540.01650.0618-0.1659-0.0178-0.0199-0.01290.10620.06050.14156.81333.1219-58.2994
92.2197-0.088-0.11263.688-0.11554.13510.0042-0.17230.19660.07780.0799-0.127-0.0563-0.1002-0.08410.3254-0.0035-0.02810.0532-0.03760.088737.1335-13.4616-23.476
101.2218-0.17970.03890.8608-0.11554.31480.0149-0.08450.0708-0.1042-0.03560.1664-0.1711-0.62650.02070.2540.0427-0.00070.3202-0.02520.172821.7658-12.0176-3.2084
114.6295-1.05951.06450.6311.52438.28840.3315-1.3986-0.01151.14040.06150.24920.9022-0.8835-0.3930.4949-0.14420.0620.64980.00080.185519.4135-23.8420.843
121.8368-0.49940.15651.5953-0.97774.083-0.0291-0.21150.32380.0040.01350.3777-0.8201-1.23470.01550.37320.24780.01970.657-0.07710.330812.8668-3.62334.3984
133.22171.1887-0.62782.21310.15062.59160.1431-0.029-0.1860.1252-0.0424-0.21080.0047-0.1274-0.10080.0674-0.0406-0.08810.25790.06070.1312-29.6735-19.5457-45.4911
141.93871.44050.07122.56472.20333.09720.07070.23010.059-0.06480.1578-0.0422-0.3388-0.0607-0.22850.0704-0.0019-0.01570.25960.11840.1141-30.6787-11.1567-44.294
1516.223-3.6339-4.35332.473-2.218.2282-0.084-0.15140.15310.15770.1324-0.4814-0.44170.4728-0.04840.2979-0.0505-0.00680.3220.01380.2506-19.2095-1.1041-24.0512
161.23060.0607-0.15451.3114-0.00013.85590.0426-0.08470.2620.2212-0.02220.2431-0.6144-0.4533-0.02040.26120.10060.08540.26270.06410.2294-39.8198-0.4864-22.6985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A135 - 239
2X-RAY DIFFRACTION2A240 - 398
3X-RAY DIFFRACTION3A399 - 413
4X-RAY DIFFRACTION4A414 - 481
5X-RAY DIFFRACTION5B135 - 219
6X-RAY DIFFRACTION6B220 - 322
7X-RAY DIFFRACTION7B323 - 441
8X-RAY DIFFRACTION8B442 - 480
9X-RAY DIFFRACTION9C135 - 239
10X-RAY DIFFRACTION10C240 - 399
11X-RAY DIFFRACTION11C400 - 410
12X-RAY DIFFRACTION12C412 - 480
13X-RAY DIFFRACTION13D135 - 213
14X-RAY DIFFRACTION14D219 - 248
15X-RAY DIFFRACTION15D249 - 255
16X-RAY DIFFRACTION16D256 - 480

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