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- PDB-4dfx: Crystal structure of myristoylated K7C catalytic subunit of cAMP-... -

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Basic information

Entry
Database: PDB / ID: 4dfx
TitleCrystal structure of myristoylated K7C catalytic subunit of cAMP-dependent protein kinase in complex with SP20 and AMP-PNP
Components(cAMP-dependent protein kinase ...Protein kinase A) x 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase / myristoylated / Phosphotransferase onto Ser/Thr / Mg / PKI / PKA Regulatory subunits / phosphorylated on S139 / T197 / S338 / myristoylated on G1 / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / MAPK6/MAPK4 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / CD209 (DC-SIGN) signaling / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / protein kinase A catalytic subunit binding / plasma membrane raft / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / protein kinase A signaling / positive regulation of gluconeogenesis / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / small GTPase binding / presynapse / cellular response to heat / manganese ion binding / postsynapse / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / magnesium ion binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / MYRISTIC ACID / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBastidas, A.C. / Steichen, J.M. / Taylor, S.S.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Role of N-terminal myristylation in the structure and regulation of cAMP-dependent protein kinase.
Authors: Bastidas, A.C. / Deal, M.S. / Steichen, J.M. / Keshwani, M.M. / Guo, Y. / Taylor, S.S.
History
DepositionJan 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: cAMP-dependent protein kinase catalytic subunit alpha
I: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9709
Polymers42,9112
Non-polymers1,0597
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-23 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.100, 79.700, 117.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CAMP-dependent protein kinase ... , 2 types, 2 molecules EI

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / CAMP-dependent pathway / PKA C-alpha


Mass: 40711.258 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-351 / Mutation: K7C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkaca, Pkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / CAMP-dependent pathway / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2199.386 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 6-25 / Mutation: N20A, A21S / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P63248

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Non-polymers , 5 types, 460 molecules

#3: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Mother liquor: 12% MPD, 100 mM Bis-Tris, Protein solution: 50 mM Bicine, 150 mM Ammonium Acetate, 10 mM DTT, 8-10 mg/mL 9% MeOH added to the well immediately before sealing. 8 uL drop size ...Details: Mother liquor: 12% MPD, 100 mM Bis-Tris, Protein solution: 50 mM Bicine, 150 mM Ammonium Acetate, 10 mM DTT, 8-10 mg/mL 9% MeOH added to the well immediately before sealing. 8 uL drop size with 1:1 protein:mother liquor, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→25.03 Å / Num. all: 99418 / Num. obs: 95939 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Redundancy: 5.3 % / Rsym value: 0.048 / Net I/σ(I): 15.8
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.359 / % possible all: 92.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→25.03 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.415 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17893 4783 5 %RANDOM
Rwork0.15549 ---
obs0.15669 90882 96.04 %-
all-94649 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.013 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 66 453 3534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223237
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9744394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5185396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52424155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25215.053567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2451518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212435
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9021.51888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45123056
X-RAY DIFFRACTIONr_scbond_it2.09131349
X-RAY DIFFRACTIONr_scangle_it3.1224.51325
X-RAY DIFFRACTIONr_rigid_bond_restr1.12433236
X-RAY DIFFRACTIONr_sphericity_free3.0133455
X-RAY DIFFRACTIONr_sphericity_bonded2.74433148
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 327 -
Rwork0.224 6327 -
obs--91.91 %
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)
10.59440.1273-0.06011.08580.45371.52120.0206-0.03510.00330.0298-0.02580.0359-0.00660.01910.00510.0204-0.0010.010.02380.0020.0462-8.4575.55-24.026
20.1823-0.7517-0.25824.51153.51414.70120.008-0.00770.069-0.03250.1116-0.29990.03690.1946-0.11960.02540.02610.00740.0506-0.00410.08063.541-6.112-32.01
32.54252.1418-0.46993.0138-0.98981.6064-0.0454-0.0682-0.14370.17050.0766-0.14130.12990.1261-0.03130.1040.0343-0.00710.0636-0.00930.0315-3.6210.275-17.332
40.0003-0.000100.000100.000300.0006-0.00250.0006-0.00010.0008-0.0034-0.00030.00020.03480.0031-0.00160.002-0.00660.0249-1.7181.873-21.028
50.00140.00120.00040.00170.00050.00030.00160.0007-0.00090.002-0.0024-0.00250.0001-0.00150.00080.0337-0.00730.01350.0273-0.01310.0384-0.045.288-20.345
60.6370.0012-0.09321.03940.47981.60620.0206-0.03470.00920.0263-0.02130.0334-0.0090.02110.00060.11050.00150.00820.12270.00870.1507-6.575.404-23.093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 350
2X-RAY DIFFRACTION2I5 - 24
3X-RAY DIFFRACTION3E402
4X-RAY DIFFRACTION4E403
5X-RAY DIFFRACTION5E404
6X-RAY DIFFRACTION6E501 - 865
7X-RAY DIFFRACTION6I101 - 138

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