4XW4

X-ray structure of PKAc with AMPPNP, SP20, calcium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Phosphoryl Transfer Reaction Snapshots in Crystals: INSIGHTS INTO THE MECHANISM OF PROTEIN KINASE A CATALYTIC SUBUNIT.

Gerlits, O.Tian, J.Das, A.Langan, P.Heller, W.T.Kovalevsky, A.

(2015) J.Biol.Chem. 290: 15538-15548

  • DOI: 10.1074/jbc.M115.643213
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To study the catalytic mechanism of phosphorylation catalyzed by cAMP-dependent protein kinase (PKA) a structure of the enzyme-substrate complex representing the Michaelis complex is of specific interest as it can shed light on the structure of the t ...

    To study the catalytic mechanism of phosphorylation catalyzed by cAMP-dependent protein kinase (PKA) a structure of the enzyme-substrate complex representing the Michaelis complex is of specific interest as it can shed light on the structure of the transition state. However, all previous crystal structures of the Michaelis complex mimics of the PKA catalytic subunit (PKAc) were obtained with either peptide inhibitors or ATP analogs. Here we utilized Ca(2+) ions and sulfur in place of the nucleophilic oxygen in a 20-residue pseudo-substrate peptide (CP20) and ATP to produce a close mimic of the Michaelis complex. In the ternary reactant complex, the thiol group of Cys-21 of the peptide is facing Asp-166 and the sulfur atom is positioned for an in-line phosphoryl transfer. Replacement of Ca(2+) cations with Mg(2+) ions resulted in a complex with trapped products of ATP hydrolysis: phosphate ion and ADP. The present structural results in combination with the previously reported structures of the transition state mimic and phosphorylated product complexes complete the snapshots of the phosphoryl transfer reaction by PKAc, providing us with the most thorough picture of the catalytic mechanism to date.


    Organizational Affiliation

    From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 hellerwt@ornl.gov.,From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 kovalevskyay@ornl.gov.,From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
A
356Mus musculusMutation(s): 0 
Gene Names: Prkaca (Pkaca)
EC: 2.7.11.11
Find proteins for P05132 (Mus musculus)
Go to UniProtKB:  P05132
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase inhibitor alpha
B
20Oryctolagus cuniculusMutation(s): 0 
Gene Names: PKIA (PRKACN1)
Find proteins for P61926 (Oryctolagus cuniculus)
Go to Gene View: PKIA
Go to UniProtKB:  P61926
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-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: 1.82 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.364α = 90.00
b = 78.816β = 90.00
c = 97.985γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data reduction
SHELXrefinement
SHELXphasing
SHELXL-97refinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references
  • Version 1.2: 2015-07-01
    Type: Database references