4WB5

Crystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.641 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural insights into mis-regulation of protein kinase A in human tumors.

Cheung, J.Ginter, C.Cassidy, M.Franklin, M.C.Rudolph, M.J.Robine, N.Darnell, R.B.Hendrickson, W.A.

(2015) Proc.Natl.Acad.Sci.USA 112: 1374-1379

  • DOI: 10.1073/pnas.1424206112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The extensively studied cAMP-dependent protein kinase A (PKA) is involved in the regulation of critical cell processes, including metabolism, gene expression, and cell proliferation; consequentially, mis-regulation of PKA signaling is implicated in t ...

    The extensively studied cAMP-dependent protein kinase A (PKA) is involved in the regulation of critical cell processes, including metabolism, gene expression, and cell proliferation; consequentially, mis-regulation of PKA signaling is implicated in tumorigenesis. Recent genomic studies have identified recurrent mutations in the catalytic subunit of PKA in tumors associated with Cushing's syndrome, a kidney disorder leading to excessive cortisol production, and also in tumors associated with fibrolamellar hepatocellular carcinoma (FL-HCC), a rare liver cancer. Expression of a L205R point mutant and a DnaJ-PKA fusion protein were found to be linked to Cushing's syndrome and FL-HCC, respectively. Here we reveal contrasting mechanisms for increased PKA signaling at the molecular level through structural determination and biochemical characterization of the aberrant enzymes. In the Cushing's syndrome disorder, we find that the L205R mutation abolishes regulatory-subunit binding, leading to constitutive, cAMP-independent signaling. In FL-HCC, the DnaJ-PKA chimera remains under regulatory subunit control; however, its overexpression from the DnaJ promoter leads to enhanced cAMP-dependent signaling. Our findings provide a structural understanding of the two distinct disease mechanisms and they offer a basis for designing effective drugs for their treatment.


    Organizational Affiliation

    New York Structural Biology Center, New York, NY 10027; jcheung@nysbc.org wayne@xtl.cumc.columbia.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
A
350Homo sapiensMutation(s): 0 
Gene Names: PRKACA (PKACA)
EC: 2.7.11.11
Find proteins for P17612 (Homo sapiens)
Go to Gene View: PRKACA
Go to UniProtKB:  P17612
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PKI (5-24)
I
20Homo sapiensMutation(s): 0 
Gene Names: PKIA (PRKACN1)
Find proteins for P61925 (Homo sapiens)
Go to Gene View: PKIA
Go to UniProtKB:  P61925
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.641 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.178α = 90.00
b = 75.091β = 90.00
c = 80.716γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
DENZOdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references
  • Version 1.2: 2015-02-11
    Type: Database references
  • Version 1.3: 2015-02-25
    Type: Derived calculations
  • Version 1.4: 2017-11-22
    Type: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary