4YGA

CDPK1, from Toxoplasma gondii, bound to inhibitory VHH-1B7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Allosteric activation of apicomplexan calcium-dependent protein kinases.

Ingram, J.R.Knockenhauer, K.E.Markus, B.M.Mandelbaum, J.Ramek, A.Shan, Y.Shaw, D.E.Schwartz, T.U.Ploegh, H.L.Lourido, S.

(2015) Proc.Natl.Acad.Sci.USA 112: E4975-E4984

  • DOI: 10.1073/pnas.1505914112

  • PubMed Abstract: 
  • Calcium-dependent protein kinases (CDPKs) comprise the major group of Ca2+-regulated kinases in plants and protists. It has long been assumed that CDPKs are activated, like other Ca2+-regulated kinases, by derepression of the kinase domain (KD). Howe ...

    Calcium-dependent protein kinases (CDPKs) comprise the major group of Ca2+-regulated kinases in plants and protists. It has long been assumed that CDPKs are activated, like other Ca2+-regulated kinases, by derepression of the kinase domain (KD). However, we found that removal of the autoinhibitory domain from Toxoplasma gondii CDPK1 is not sufficient for kinase activation. From a library of heavy chain-only antibody fragments (VHHs), we isolated an antibody (1B7) that binds TgCDPK1 in a conformation-dependent manner and potently inhibits it. We uncovered the molecular basis for this inhibition by solving the crystal structure of the complex and simulating, through molecular dynamics, the effects of 1B7-kinase interactions. In contrast to other Ca2+-regulated kinases, the regulatory domain of TgCDPK1 plays a dual role, inhibiting or activating the kinase in response to changes in Ca2+ concentrations. We propose that the regulatory domain of TgCDPK1 acts as a molecular splint to stabilize the otherwise inactive KD. This dependence on allosteric stabilization reveals a novel susceptibility in this important class of parasite enzymes.


    Organizational Affiliation

    Whitehead Institute for Biomedical Research, Cambridge, MA 02142;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-domain protein kinase 1
A, C, E, G
516Toxoplasma gondiiGene Names: CDPK1
Find proteins for Q9BJF5 (Toxoplasma gondii)
Go to UniProtKB:  Q9BJF5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VHH-1B7
B, D, F, H
141N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, E, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • Space Group: P 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/219 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 76.920α = 88.71
b = 91.067β = 108.27
c = 106.641γ = 90.26
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/Office of the DirectorUnited States1DP5OD017892

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-09
    Type: Database references
  • Version 1.2: 2015-09-23
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations