6M7Z

A divergent kinase lacking the glycine-rich loop regulates membrane ultrastructure of the Toxoplasma parasitophorous vacuole

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Divergent kinase regulates membrane ultrastructure of theToxoplasmaparasitophorous vacuole.

Beraki, T., Hu, X., Broncel, M., Young, J.C., O'Shaughnessy, W.J., Borek, D., Treeck, M., Reese, M.L.

(2019) Proc Natl Acad Sci U S A 116: 6361-6370

  • DOI: 10.1073/pnas.1816161116
  • Primary Citation of Related Structures:  
    6M7Z

  • PubMed Abstract: 

    • Apicomplexan parasites replicate within a protective organelle, called the parasitophorous vacuole (PV). The Toxoplasma gondii PV is filled with a network of tubulated membranes, which are thought to facilitate trafficking of effectors and nutrients ...

    Apicomplexan parasites replicate within a protective organelle, called the parasitophorous vacuole (PV). The Toxoplasma gondii PV is filled with a network of tubulated membranes, which are thought to facilitate trafficking of effectors and nutrients. Despite being critical to parasite virulence, there is scant mechanistic understanding of the network's functions. Here, we identify the parasite-secreted kinase WNG1 (With-No-Gly-loop) as a critical regulator of tubular membrane biogenesis. WNG1 family members adopt an atypical protein kinase fold lacking the glycine rich ATP-binding loop that is required for catalysis in canonical kinases. Unexpectedly, we find that WNG1 is an active protein kinase that localizes to the PV lumen and phosphorylates PV-resident proteins, several of which are essential for the formation of a functional intravacuolar network. Moreover, we show that WNG1-dependent phosphorylation of these proteins is required for their membrane association, and thus their ability to tubulate membranes. Consequently, WNG1 knockout parasites have an aberrant PV membrane ultrastructure. Collectively, our results describe a unique family of Toxoplasma kinases and implicate phosphorylation of secreted proteins as a mechanism of regulating PV development during parasite infection.

    Organizational Affiliation: 

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bradyzoite pseudokinase 1
A, B, C, D, E, F
A, B, C, D, E, F
319Toxoplasma gondii RHMutation(s): 0 
Gene Names: BPK1
EC: 2.7.99.1
UniProt
Find proteins for A0A7J6KD88 (Toxoplasma gondii)
Explore A0A7J6KD88 
Go to UniProtKB:  A0A7J6KD88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7J6KD88
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
T [auth E],
U [auth E],
X [auth F],
Y [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
S [auth C],
V [auth E],
W [auth E]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.466α = 90
b = 123.068β = 90
c = 86.615γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDEphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB1553334
Robert A. Welch FoundationUnited StatesI-1936-20170325

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence