Crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium falciparum - Apo form

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structures of the cGMP-dependent protein kinase in malaria parasites reveal a unique structural relay mechanism for activation.

El Bakkouri, M.Kouidmi, I.Wernimont, A.K.Amani, M.Hutchinson, A.Loppnau, P.Kim, J.J.Flueck, C.Walker, J.R.Seitova, A.Senisterra, G.Kakihara, Y.Kim, C.Blackman, M.J.Calmettes, C.Baker, D.A.Hui, R.

(2019) Proc Natl Acad Sci U S A 116: 14164-14173

  • DOI: https://doi.org/10.1073/pnas.1905558116
  • Primary Citation of Related Structures:  
    5DYK, 5DYL, 5DZC, 5E16

  • PubMed Abstract: 

    The cyclic guanosine-3',5'-monophosphate (cGMP)-dependent protein kinase (PKG) was identified >25 y ago; however, efforts to obtain a structure of the entire PKG enzyme or catalytic domain from any species have failed. In malaria parasites, cooperative activation of PKG triggers crucial developmental transitions throughout the complex life cycle. We have determined the cGMP-free crystallographic structures of PKG from Plasmodium falciparum and Plasmodium vivax , revealing how key structural components, including an N-terminal autoinhibitory segment (AIS), four predicted cyclic nucleotide-binding domains (CNBs), and a kinase domain (KD), are arranged when the enzyme is inactive. The four CNBs and the KD are in a pentagonal configuration, with the AIS docked in the substrate site of the KD in a swapped-domain dimeric arrangement. We show that although the protein is predominantly a monomer (the dimer is unlikely to be representative of the physiological form), the binding of the AIS is necessary to keep Plasmodium PKG inactive. A major feature is a helix serving the dual role of the N-terminal helix of the KD as well as the capping helix of the neighboring CNB. A network of connecting helices between neighboring CNBs contributes to maintaining the kinase in its inactive conformation. We propose a scheme in which cooperative binding of cGMP, beginning at the CNB closest to the KD, transmits conformational changes around the pentagonal molecule in a structural relay mechanism, enabling PKG to orchestrate rapid, highly regulated developmental switches in response to dynamic modulation of cGMP levels in the parasite.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CGMP-dependent protein kinase853Plasmodium falciparumMutation(s): 0 
Gene Names: PF3D7_1436600
Find proteins for Q8I719 (Plasmodium falciparum (isolate 3D7))
Explore Q8I719 
Go to UniProtKB:  Q8I719
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I719
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.509α = 90
b = 127.284β = 90
c = 215.104γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2019-11-13
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description