Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.32 kDa 
• Atom Count: 6669 
• Modelled Residue Count: 809 
• Deposited Residue Count: 853 
• Unique protein chains: 1

5DYK

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

• PDB DOI: 10.2210/pdb5DYK/pdb
• Entry: 5DYK supersedes: 4MYJ

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-09-24 Released: 2015-11-04 
• Deposition Author(s): Wernimont, A.K., Tempel, W., He, H., Seitova, A., Hills, T., Neculai, A.M., Baker, D.A., Flueck, C., Kettleborough, C.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Hutchinson, A., El Bakkouri, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.240 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

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

• PubMed: 31239348 
• DOI: 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.

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Organizational Affiliation: 

Toronto General Hospital Research Institute, Toronto, ON M5G 2C4, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CGMP-dependent protein kinase	A	853	Plasmodium falciparum	Mutation(s): 0  Gene Names: PF3D7_1436600 EC: 2.7.11.12
UniProt
Find proteins for Q8I719 (Plasmodium falciparum (isolate 3D7)) Explore Q8I719  Go to UniProtKB:  Q8I719

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 94.509	α = 90
b = 127.284	β = 90
c = 215.104	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-09-24 
• Released Date: 2015-11-04 
Deposition Author(s): Wernimont, A.K., Tempel, W., He, H., Seitova, A., Hills, T., Neculai, A.M., Baker, D.A., Flueck, C., Kettleborough, C.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Hutchinson, A., El Bakkouri, M., Structural Genomics Consortium (SGC)
• This entry supersedes: 4MYJ

Revision History  

• 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