6E21

Joint X-ray/neutron structure of PKAc with products Sr2-ADP and phosphorylated peptide SP20


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Zooming in on protons: Neutron structure of protein kinase A trapped in a product complex.

Gerlits, O.Weiss, K.L.Blakeley, M.P.Veglia, G.Taylor, S.S.Kovalevsky, A.

(2019) Sci Adv 5: eaav0482-eaav0482

  • DOI: 10.1126/sciadv.aav0482

  • PubMed Abstract: 
  • The question vis-à-vis the chemistry of phosphoryl group transfer catalyzed by protein kinases remains a major challenge. The neutron diffraction structure of the catalytic subunit of cAMP-dependent protein kinase (PKA-C) provides a more complete che ...

    The question vis-à-vis the chemistry of phosphoryl group transfer catalyzed by protein kinases remains a major challenge. The neutron diffraction structure of the catalytic subunit of cAMP-dependent protein kinase (PKA-C) provides a more complete chemical portrait of key proton interactions at the active site. By using a high-affinity protein kinase substrate (PKS) peptide, we captured the reaction products, dephosphorylated nucleotide [adenosine diphosphate (ADP)] and phosphorylated PKS (pPKS), bound at the active site. In the complex, the phosphoryl group of the peptide is protonated, whereas the carboxyl group of the catalytic Asp 166 is not. Our structure, including conserved waters, shows how the peptide links the distal parts of the cleft together, creating a network that engages the entire molecule. By comparing slow-exchanging backbone amides to those determined by the NMR analysis of PKA-C with ADP and inhibitor peptide (PKI), we identified exchangeable amides that likely distinguish catalytic and inhibited states.


    Related Citations: 
    • Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
      Adams, P.D.,Mustyakimov, M.,Afonine, P.V.,Langan, P.
      (2009) Acta Crystallogr. D Biol. Crystallogr. 65: 567


    Organizational Affiliation

    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.,Large Scale Structures Group, Institut Laue-Langevin, Grenoble Cedex 9, 38042, France.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA.




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
pSP20
B
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
A
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A, B
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
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: NEUTRON DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.332α = 90.00
b = 79.898β = 90.00
c = 100.292γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHASERphasing
LSCALEdata scaling
LAUEGENdata reduction
HKL-3000data reduction
CNSphasing
nCNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Data collection, Database references