4HPU

Crystal structure of the catalytic subunit of cAMP-dependent protein kinase displaying partial phosphoryl transfer of AMP-PNP onto a substrate peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Phosphoryl transfer by protein kinase a is captured in a crystal lattice.

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

(2013) J Am Chem Soc 135: 4788-4798

  • DOI: 10.1021/ja312237q
  • Primary Citation of Related Structures:  
    4HPT, 4HPU

  • PubMed Abstract: 
  • The catalytic (C) subunit of cAMP-dependent protein kinase (PKA) is a serine/threonine kinase responsible for most of the effects of cAMP signaling, and PKA serves as a prototype for the entire kinase family. Despite multiple studies of PKA, the step ...

    The catalytic (C) subunit of cAMP-dependent protein kinase (PKA) is a serine/threonine kinase responsible for most of the effects of cAMP signaling, and PKA serves as a prototype for the entire kinase family. Despite multiple studies of PKA, the steps involved in phosphoryl transfer, the roles of the catalytically essential magnesium ions, and the processes that govern the rate-limiting step of ADP release are unresolved. Here we identified conditions that yielded slow phosphoryl transfer of the γ-phosphate from the generally nonhydrolyzable analog of ATP, adenosine-5'-(β,γ-imido)triphosphate (AMP-PNP), onto a substrate peptide within protein crystals. By trapping both products in the crystal lattice, we now have a complete resolution profile of all the catalytic steps. One crystal structure refined to 1.55 Å resolution shows two states of the protein with 55% displaying intact AMP-PNP and an unphosphorylated substrate and 45% displaying transfer of the γ-phosphate of AMP-PNP onto the substrate peptide yielding AMP-PN and a phosphorylated substrate. Another structure refined to 2.15 Å resolution displays complete phosphoryl transfer to the substrate. These structures, in addition to trapping both products in the crystal lattice, implicate one magnesium ion, previously termed Mg2, as the more stably bound ion. Following phosphoryl transfer, Mg2 recruits a water molecule to retain an octahedral coordination geometry suggesting the strong binding character of this magnesium ion, and Mg2 remains in the active site following complete phosphoryl transfer while Mg1 is expelled. Loss of Mg1 may thus be an important part of the rate-limiting step of ADP release.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaE350Mus musculusMutation(s): 0 
Gene Names: PrkacaPkaca
EC: 2.7.11.11
Find proteins for P05132 (Mus musculus)
Explore P05132 
Go to UniProtKB:  P05132
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor alphaI20Mus musculusMutation(s): 2 
Gene Names: Pkia
Find proteins for P63248 (Mus musculus)
Explore P63248 
Go to UniProtKB:  P63248
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
E, I
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MYR
Query on MYR

Download CCD File 
E
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.69α = 90
b = 79.8β = 90
c = 98.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references
  • Version 1.2: 2013-04-03
    Changes: Other
  • Version 1.3: 2013-04-10
    Changes: Database references
  • Version 1.4: 2017-11-15
    Changes: Advisory, Refinement description