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- PDB-2h9r: Docking and dimerization domain (D/D) of the regulatory subunit o... -

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Basic information

Entry
Database: PDB / ID: 2h9r
TitleDocking and dimerization domain (D/D) of the regulatory subunit of the Type II-alpha cAMP-dependent protein kinase A associated with a Peptide derived from an A-kinase anchoring protein (AKAP)
Components
  • 22-mer from A-kinase anchor protein 5
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsTRANSFERASE / AKAP / PKA / signal transduction / 4-helix bundle / helix-loop-helix / protein-peptide complex
Function / homology
Function and homology information


positive regulation of meiotic cell cycle process involved in oocyte maturation / positive regulation of endosome to plasma membrane protein transport / : / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Hedgehog 'off' state / PKA activation ...positive regulation of meiotic cell cycle process involved in oocyte maturation / positive regulation of endosome to plasma membrane protein transport / : / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Hedgehog 'off' state / PKA activation / postsynaptic recycling endosome membrane / postsynaptic recycling endosome / cAMP-dependent protein kinase regulator activity / positive regulation of calcium ion import across plasma membrane / ROBO receptors bind AKAP5 / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / calcineurin-NFAT signaling cascade / nucleotide-activated protein kinase complex / positive regulation of calcineurin-NFAT signaling cascade / GABA receptor binding / negative regulation of adenylate cyclase activity / protein phosphatase 2B binding / Trafficking of AMPA receptors / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / negative regulation of cAMP/PKA signal transduction / Vasopressin regulates renal water homeostasis via Aquaporins / germinal vesicle / cAMP-dependent protein kinase inhibitor activity / beta-2 adrenergic receptor binding / cAMP-dependent protein kinase complex / protein kinase A binding / small molecule binding / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / adenylate cyclase binding / plasma membrane raft / axoneme / excitatory synapse / glutamate receptor binding / cAMP binding / dendrite membrane / T-tubule / positive regulation of long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / modulation of chemical synaptic transmission / SH3 domain binding / cytoplasmic side of plasma membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / scaffold protein binding / chemical synaptic transmission / molecular adaptor activity / dendritic spine / postsynaptic membrane / calmodulin binding / postsynaptic density / membrane raft / protein domain specific binding / synapse / dendrite / ubiquitin protein ligase binding / centrosome / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / protein-containing complex / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
A kinase-anchoring protein AKAP5 and AKAP12, calmodulin (CaM)-binding motif / A-kinase anchor protein 5 / WSK motif / A kinase-anchoring proteins AKAP-5 and AKAP-12 calmodulin (CaM)-binding motif profile. / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / 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 ...A kinase-anchoring protein AKAP5 and AKAP12, calmodulin (CaM)-binding motif / A-kinase anchor protein 5 / WSK motif / A kinase-anchoring proteins AKAP-5 and AKAP-12 calmodulin (CaM)-binding motif profile. / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / 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. / 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 / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit / A-kinase anchor protein 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsNewlon, M.G. / Roy, M. / Morikis, D. / Hausken, Z.E. / Coghlan, V. / Scott, J.D. / Jennings, P.A.
CitationJournal: Embo J. / Year: 2001
Title: A novel mechanism of PKA anchoring revealed by solution structures of anchoring complexes.
Authors: Newlon, M.G. / Roy, M. / Morikis, D. / Carr, D.W. / Westphal, R. / Scott, J.D. / Jennings, P.A.
History
DepositionJun 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase type II-alpha regulatory subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
C: 22-mer from A-kinase anchor protein 5


Theoretical massNumber of molelcules
Total (without water)13,1803
Polymers13,1803
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide cAMP-dependent protein kinase type II-alpha regulatory subunit


Mass: 5398.181 Da / Num. of mol.: 2
Fragment: N-terminal docking and dimerization domain, residues 4-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RIIA(1-44) / Plasmid: PET-16B / Production host: Escherichia coli (E. coli) / References: UniProt: P12368, EC: 2.7.1.37
#2: Protein/peptide 22-mer from A-kinase anchor protein 5 / AKAP79(391-412) / AKAP75(391-412)


Mass: 2383.800 Da / Num. of mol.: 1 / Fragment: PKA-RII subunit binding domain / Source method: obtained synthetically
Details: The peptide has been generated by solid phase peptide synthesis.; This sequence occurs naturally in humans.
References: UniProt: P24588

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: This structure was determined using standard 2d and 3d heteronuclear and homonuclear techniques.

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Sample preparation

DetailsContents: 2mM RII-alpha(1-44); 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1271 restraints, 1150 are noe-derived distance restraints, 50 dihedral angle restraints,71 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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