Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.14 kDa 
• Atom Count: 3304 
• Modelled Residue Count: 370 
• Deposited Residue Count: 370 
• Unique protein chains: 2

4DFZ

Crystal structure of myristoylated K7C catalytic subunit of cAMP-dependent protein kinase in complex with SP20

• PDB DOI: 10.2210/pdb4DFZ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-24 Released: 2012-06-06 
• Deposition Author(s): Bastidas, A.C., Steichen, J.M., Taylor, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Role of N-terminal myristylation in the structure and regulation of cAMP-dependent protein kinase.

Bastidas, A.C., Deal, M.S., Steichen, J.M., Keshwani, M.M., Guo, Y., Taylor, S.S.

(2012) J Mol Biol 422: 215-229

• PubMed: 22617327 
• DOI: 10.1016/j.jmb.2012.05.021
• Primary Citation of Related Structures:  
  4DFX, 4DFZ, 4DG0, 4DG2


• PubMed Abstract: 
  

The catalytic (C) subunit of cAMP-dependent protein kinase [protein kinase A (PKA)] is a major target of cAMP signaling, and its regulation is of fundamental importance to biological processes. One mode of regulation is N-myristylation, which has eluded structural and functional characterization so far because most crystal structures are of the non-myristylated enzyme, are phosphorylated on Ser10, and generally lack electron density for the first 13 residues. We crystallized myristylated wild-type (WT) PKA and a K7C mutant as binary (bound to a substrate peptide) and ternary [bound to a substrate peptide and adenosine-5'-(β,γ-imido)triphosphate] complexes. There was clear electron density for the entire N-terminus in the binary complexes, both refined to 2.0 Å, and K7C ternary complex, refined to 1.35 Å. The N-termini in these three structures display a novel conformation with a previously unseen helix from residues 1 to 7. The K7C mutant appears to have a more stable N-terminus, and this correlated with a significant decrease in the B-factors for the N-terminus in the myr-K7C complexes compared to the WT binary complex. The N-terminus of the myristylated WT ternary complex, refined to 2.0 Å, was disordered as in previous structures. In addition to a more ordered N-terminus, the myristylated K7C mutant exhibited a 53% increase in k(cat). The effect of nucleotide binding on the structure of the N-terminus in the WT protein and the kinetic changes in the K7C protein suggest that myristylation or occupancy of the myristyl binding pocket may serve as a site for allosteric regulation in the C-subunit.

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Organizational Affiliation: 

Department of Pharmacology, University of California San Diego, San Diego, CA 92093, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A [auth E]	350	Mus musculus	Mutation(s): 1  Gene Names: Prkaca, Pkaca EC: 2.7.11.11
UniProt
Find proteins for P05132 (Mus musculus) Explore P05132  Go to UniProtKB:  P05132

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B [auth I]	20	Mus musculus	Mutation(s): 2  Gene Names: Pkia
UniProt & NIH Common Fund Data Resources
Find proteins for P63248 (Mus musculus) Explore P63248  Go to UniProtKB:  P63248
IMPC:  MGI:104747

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYR	C [auth E]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A [auth E]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A [auth E]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.46	α = 90
b = 79.63	β = 90
c = 118.06	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-24 
• Released Date: 2012-06-06 
Deposition Author(s): Bastidas, A.C., Steichen, J.M., Taylor, S.S.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references