Keywords

CDPK, CLD, JC, Calmodulin-like Domain, Domain Swap, Kinase Regulation

Reference

DOI: 10.1016/j.jmb.2005.11.093

Abstract

Calcium-dependent protein kinases (CDPKs) are Ca2+-regulated kinases unique to plants and some protozoa. They contain an autoinhibitory junction (J) domain and a tethered calmodulin-like domain (CaM-LD).
This study reports the 2.0 Å X-ray structure of Arabidopsis AtCPK1’s J-CaM-LD region, showing a symmetric, domain-swapped dimer involving J-CaM-LD interactions.
Although monomeric in solution, the domain-swap reveals how J region engages specifically with the C-lobe of CaM-LD, offering a unique CaM-target recognition model distinct from classical CaM wrapping.
This structure suggests strong J–C-lobe interactions may persist even at basal Ca2+, pointing to a unique regulatory mechanism in CDPKs compared to other CaM superfamily members.

Notes

1. Key Features of the J-CaM-LD Structure

  • Crystal structure captured a homodimer via domain swap, but monomeric in solution (no dimer even at 2 mM protein concentration).
  • J region forms an amphipathic α-helix, primarily interacting with the C-lobe of CaM-LD.
  • Unlike CaM, no wrap-around binding observed.
  • The structure reveals a fixed relative orientation of N- and C-lobes, contrasting with CaM’s flexible lobes.

2. Critical Interactions at the Interface

  • Hydrophobic interactions:
    • Phe436 (J) as key anchor into C-lobe hydrophobic pocket.
    • Other J residues (Met439, Ala440, Val443, Ile444) engage in van der Waals interactions.
  • Electrostatic interactions:
    • Lys437 forms H-bond with Gln587 of C-lobe.
  • Combined hydrophobic & electrostatic network stabilizing J–C-lobe binding.

Fancy insight: Unlike CaM’s broad flexibility and promiscuous target binding, CDPK’s CaM-LD uses a specific, C-lobe-focused recognition mode, restricting its interaction style and perhaps fine-tuning signaling fidelity.

3. Domain-Swap Observations and Regulatory Implications

  • Domain-swapped dimer observed in crystals—J helix of one monomer binds C-lobe of the other.
  • Suggests possible intermolecular mimic of intramolecular interactions in full-length CDPK.
  • While swap does not occur in solution, it offers a structural model for J–CaM-LD recognition within the same molecule.
  • Phe436 as key anchor but no second anchor—explains why J helix binds but doesn’t wrap around C-lobe like CaM-target complexes.

4. Mechanistic Differences from CaM and Broader Family Insights

  • Absence of conserved Met residues in CaM-LD that are crucial in CaM for target flexibility.
  • Explains lack of promiscuity and strict target recognition in CDPK.
  • Tethered regulatory domains (like JC) evolve as a unit, allowing co-evolution and tighter functional tuning.

Evolutionary insight: CDPK CaM-LD is customized to its own kinase, unlike CaM’s need for broad target engagement—highlighting an evolutionary trade-off for specificity.

5. Activation Model: Unique CDPK Mechanism

  • J–CaM-LD interaction dominates even at low Ca2+, contrasting with CaM’s need for full Ca2+ occupancy for binding.
  • Suggests C-lobe may remain bound and primed, with N-lobe acting as Ca2+ sensor for activation.
  • Activation may involve conformational changes in N-lobe and J displacement, not full unwrapping like in CaM.

Take-home Messages

  • J-CaM-LD domain swap offers unprecedented structural insights into CDPK autoregulation.
  • C-lobe exclusive binding of J helix distinguishes CDPK from classical CaM-target interactions.
  • Fixed lobe orientation and absence of flexible Met anchors limit promiscuity—tuning CDPK for specific intramolecular control.
  • Co-evolved tethered regulatory apparatus allows precise kinase control—model for future synthetic kinase designs.
  • CDPK as a model of “hard-wired” CaM-LD signaling, breaking classical CaM mold!

PDB & PyMOL

PDB ID: 2AAO

  • Hydrophobic core: Met439, Ala440, Val443, Ile444
  • Key anchor: Phe436
  • Electrostatic points: Lys437 → Gln587
  • Suggested PyMOL command (for figure making):
fetch 2AAO
hide everything
show cartoon
color lightblue, chain A
color lightpink, chain B
show sticks, resi 436+439+440+443+444+437+587
set stick_radius, 0.2