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- PDB-1l6e: Solution structure of the docking and dimerization domain of prot... -

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Basic information

Entry
Database: PDB / ID: 1l6e
TitleSolution structure of the docking and dimerization domain of protein kinase A II-alpha (RIIalpha D/D). Alternatively called the N-terminal dimerization domain of the regulatory subunit of protein kinase A.
ComponentscAMP-dependent protein kinase Type II-alpha regulatory chainCAMP-dependent pathway
KeywordsTRANSFERASE / Four-helix bundle / helix-loop-helix / regulatory subunit / dimerization / docking / anchoring
Function / homology
Function and homology information


PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state / cAMP-dependent protein kinase regulator activity / Factors involved in megakaryocyte development and platelet production / nucleotide-activated protein kinase complex ...PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state / cAMP-dependent protein kinase regulator activity / Factors involved in megakaryocyte development and platelet production / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / beta-2 adrenergic receptor binding / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / plasma membrane raft / small molecule binding / cAMP binding / T-tubule / regulation of protein phosphorylation / modulation of chemical synaptic transmission / protein domain specific binding / centrosome / glutamatergic synapse / synapse / ubiquitin protein ligase binding / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Hybrid distance geometry-dynamical simulated annealing, refinement protocol for monomer structure determination, with 457 NOE-derived distance restraints (185 intra-residue, i-j=0; 136 sequential, |i-j|=1; 95 medium range, 1<|i-j|<5; 41 long range, |i-j|>4), 19 distance restraints representing hydrogen bonds (entered as 2 distances each), 25 phi-, 5 chi1-torsion angle restraints. Molecular dynamical simulated annealing protocol for dimer structure determination, using 505 NOE-derived distance restraints (185 intra-residue, i-j=0; 136 sequential, |i-j|=1; 95 medium range, 1<|i-j|<5; 25 long range, |i-j|>4; 38 inter-molecular; 26 ambiguous), 19 distance restraints representing hydrogen bonds (entered as 2 distances each), 25 phi-, 5 chi1-torsion angle restraints.
AuthorsMorikis, D. / Roy, M. / Newlon, M.G. / Scott, J.D. / Jennings, P.A.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: Electrostatic properties of the structure of the docking and dimerization domain of protein kinase A IIalpha
Authors: Morikis, D. / Roy, M. / Newlon, M.G. / Scott, J.D. / Jennings, P.A.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: The molecular basis for protein kinase A anchoring revealed by solution NMR.
Authors: Newlon, M.G. / Roy, M. / Morikis, D. / Hausken, Z.E. / Coghlan, V. / Scott, J.D. / Jennings, P.A.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: The A-kinase anchoring domain of type II-alpha cAMP-dependent protein kinase is highly helical.
Authors: Newlon, M.G. / Roy, M. / Hausken, Z.E. / Scott, J.D. / Jennings, P.A.
History
DepositionMar 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE THE FIRST 3 RESIDUES ARE DIFFERENT DUE TO RECOMBINANT EXPRESSION AND PROTEOLYTIC CLEAVAGE.

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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 chain
B: cAMP-dependent protein kinase Type II-alpha regulatory chain


Theoretical massNumber of molelcules
Total (without water)10,7962
Polymers10,7962
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 49structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide cAMP-dependent protein kinase Type II-alpha regulatory chain / CAMP-dependent pathway


Mass: 5398.181 Da / Num. of mol.: 2 / Fragment: N-terminal docking and dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RIIA(1-44) / Plasmid: PET-16B / Production host: Escherichia coli (E. coli) / References: UniProt: P12367, EC: 2.7.1.37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: This structure was determined using standard homonuclear, heteronuclear, and triple resonance spectroscopy, and 3D 13C-edited(w2)-12C-filtered(w1)/13C-filtered(w3) NOESY.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM dimer protein in 20 mM sodium phosphate buffer, 90%H2O-10% D2O, at pH 4 and temperature 298K90% H2O/10% D2O
21mM dimer protein 15N in 20 mM sodium phosphate buffer, 90%H2O-10% D2O, at pH 4 and temperature 298K90% H2O/10% D2O
31mM dimer protein 13C-15N in 20 mM sodium phosphate buffer, 90%H2O-10% D2O, at pH 4 and temperature 298K90% H2O/10% D2O
4Mixture of 2mM unlabeled and 2 mM 13C-15N labeled sample unfolded in 5 M guanadine hydrochloride and refolded in 20 mM sodium phosphate buffer, 90% H2O-10% D2O, at pH 4 and temperature 298K90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.012 4 1 atm298 K
20.012 4 1 atm298 K
30.012 4 1 atm298 K
40.012 4 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.T.structure solution
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: Hybrid distance geometry-dynamical simulated annealing, refinement protocol for monomer structure determination, with 457 NOE-derived distance restraints (185 intra-residue, i-j=0; 136 ...Method: Hybrid distance geometry-dynamical simulated annealing, refinement protocol for monomer structure determination, with 457 NOE-derived distance restraints (185 intra-residue, i-j=0; 136 sequential, |i-j|=1; 95 medium range, 1
Software ordinal: 1
Details: Filtered NOESY spectrum on a 50% unlabeled-50% 13C-15N-labeled sample was used to obtain inter-molecular NOE contacts of the homodimer. Other NOEs were classified as intra-molecular and ambiguous.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 49 / Conformers submitted total number: 24

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