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- PDB-2qvs: Crystal Structure of Type IIa Holoenzyme of cAMP-dependent Protei... -

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Basic information

Entry
Database: PDB / ID: 2qvs
TitleCrystal Structure of Type IIa Holoenzyme of cAMP-dependent Protein Kinase
Components
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
  • cAMP-dependent protein kinase, alpha-catalytic subunit
Keywordstransferase/transferase regulator / cAMP-dependent protein kinase / Type IIa holoenzyme / isoform diversity / Alternative splicing / ATP-binding / Cytoplasm / Lipoprotein / Myristate / Nucleotide-binding / Nucleus / Phosphorylation / Serine/threonine-protein kinase / Transferase / Acetylation / cAMP-binding / transferase-transferase regulator COMPLEX
Function / homology
Function and homology information


spontaneous exocytosis of neurotransmitter / negative regulation of meiotic cell cycle / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / regulation of protein processing / DARPP-32 events / Rap1 signalling / regulation of protein kinase activity / PKA activation ...spontaneous exocytosis of neurotransmitter / negative regulation of meiotic cell cycle / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / regulation of protein processing / DARPP-32 events / Rap1 signalling / regulation of protein kinase activity / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to parathyroid hormone stimulus / GPER1 signaling / protein localization to lipid droplet / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Factors involved in megakaryocyte development and platelet production / cAMP-dependent protein kinase regulator activity / Hedgehog 'off' state / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / regulation of cellular respiration / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / RET signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / Mitochondrial protein degradation / cellular response to cold / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / interleukin-2-mediated signaling pathway / Ion homeostasis / mesoderm formation / cAMP-dependent protein kinase inhibitor activity / TORC1 signaling / potassium channel inhibitor activity / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / positive regulation of triglyceride catabolic process / negative regulation of glycolytic process / beta-2 adrenergic receptor binding / cAMP-dependent protein kinase activity / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / neural tube closure / negative regulation of glycolytic process through fructose-6-phosphate / sperm capacitation / regulation of osteoblast differentiation / peptidyl-threonine phosphorylation / protein kinase A regulatory subunit binding / ciliary base / protein kinase A catalytic subunit binding / small molecule binding / intracellular potassium ion homeostasis / plasma membrane raft / axoneme / cAMP/PKA signal transduction / postsynaptic modulation of chemical synaptic transmission / cAMP binding / sperm flagellum / regulation of synaptic transmission, glutamatergic / negative regulation of cAMP/PKA signal transduction / positive regulation of gluconeogenesis / cellular response to nutrient levels / positive regulation of protein export from nucleus / negative regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / negative regulation of smoothened signaling pathway / positive regulation of phagocytosis / T-tubule / acrosomal vesicle / sperm midpiece / regulation of proteasomal protein catabolic process / negative regulation of protein localization to chromatin / lipid droplet / cellular response to glucose stimulus / neuromuscular junction / regulation of microtubule cytoskeleton organization / positive regulation of cholesterol biosynthetic process / peptidyl-serine phosphorylation / modulation of chemical synaptic transmission / small GTPase binding / mRNA processing / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / manganese ion binding / protein autophosphorylation / cellular response to heat / presynapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of cell cycle / protein kinase activity / protein phosphorylation
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Jelly Rolls / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Jelly Rolls / 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 / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase type II-alpha regulatory subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWu, J. / Brown, S.H.J. / von Daake, S. / Taylor, S.S.
CitationJournal: Science / Year: 2007
Title: PKA type IIalpha holoenzyme reveals a combinatorial strategy for isoform diversity.
Authors: Wu, J. / Brown, S.H.J. / von Daake, S. / Taylor, S.S.
History
DepositionAug 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: cAMP-dependent protein kinase, alpha-catalytic subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)75,9582
Polymers75,9582
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.9, 92.9, 118.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40657.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkaca, Pkaca / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05132, cAMP-dependent protein kinase
#2: Protein cAMP-dependent protein kinase type II-alpha regulatory subunit


Mass: 35301.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkar2a / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12367
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.9 M sodium formate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2005 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 34006 / Num. obs: 33730 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 31.3 Å2 / Rsym value: 0.076 / Net I/σ(I): 18.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3232 / Rsym value: 0.454 / % possible all: 95.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATP

1atp


Resolution: 2.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1309 -RANDOM
Rwork0.212 ---
all-34006 --
obs-26790 78.4 %-
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å20 Å20 Å2
2--3.65 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4878 0 0 181 5059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.256 54 -
Rwork0.263 --
obs-1260 95.5 %

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