Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 43.10 kDa 
• Atom Count: 3245 
• Modelled Residue Count: 359 
• Deposited Residue Count: 368 
• Unique protein chains: 2

3QAL

Crystal Structure of Arg280Ala mutant of Catalytic subunit of cAMP-dependent Protein Kinase

• PDB DOI: 10.2210/pdb3QAL/pdb

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


• Deposited: 2011-01-11 Released: 2011-12-07 
• Deposition Author(s): Yang, J., Wu, J., Steichen, J., Taylor, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.194 
• R-Value Work: 0.176 

Literature

A conserved Glu-Arg salt bridge connects coevolved motifs that define the eukaryotic protein kinase fold.

Yang, J., Wu, J., Steichen, J.M., Kornev, A.P., Deal, M.S., Li, S., Sankaran, B., Woods, V.L., Taylor, S.S.

(2012) J Mol Biol 415: 666-679

• PubMed: 22138346 
• DOI: 10.1016/j.jmb.2011.11.035
• Primary Citation of Related Structures:  
  3QAL, 3QAM


• PubMed Abstract: 
  

Eukaryotic protein kinases (EPKs) feature two coevolved structural segments, the Activation segment, which starts with the Asp-Phe-Gly (DFG) and ends with the Ala-Pro-Glu (APE) motifs, and the helical GHI subdomain that comprises αG-αH-αI helices. Eukaryotic-like kinases have a much shorter Activation segment and lack the GHI subdomain. They thus lack the conserved salt bridge interaction between the APE Glu and an Arg from the GHI subdomain, a hallmark signature of EPKs. Although the conservation of this salt bridge in EPKs is well known and its implication in diseases has been illustrated by polymorphism analysis, its function has not been carefully studied. In this work, we use murine cAMP-dependent protein kinase (protein kinase A) as the model enzyme (Glu208 and Arg280) to examine the role of these two residues. We showed that Ala replacement of either residue caused a 40- to 120-fold decrease in catalytic efficiency of the enzyme due to an increase in K(m)(ATP) and a decrease in k(cat). Crystal structures, as well as solution studies, also demonstrate that this ion pair contributes to the hydrophobic network and stability of the enzyme. We show that mutation of either Glu or Arg to Ala renders both mutant proteins less effective substrates for upstream kinase phosphoinositide-dependent kinase 1. We propose that the Glu208-Arg280 pair serves as a center hub of connectivity between these two structurally conserved elements in EPKs. Mutations of either residue disrupt communication not only between the two segments but also within the rest of the molecule, leading to altered catalytic activity and enzyme regulation.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, 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
Protein kinase inhibitor	B [auth I]	18	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P63248 (Mus musculus) Explore P63248  Go to UniProtKB:  P63248
IMPC:  MGI:104747

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth E]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	D [auth E], E	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.70 Å
• R-Value Free: 0.194 
• R-Value Work: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.758	α = 90
b = 80.082	β = 90
c = 97.715	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-11 
• Released Date: 2011-12-07 
Deposition Author(s): Yang, J., Wu, J., Steichen, J., Taylor, S.S.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references