Hybrid histidine kinase activation by cyclic di-GMP-mediated domain liberation

Proc Natl Acad Sci U S A. 2020 Jan 14;117(2):1000-1008. doi: 10.1073/pnas.1911427117. Epub 2019 Dec 27.


Cytosolic hybrid histidine kinases (HHKs) constitute major signaling nodes that control various biological processes, but their input signals and how these are processed are largely unknown. In Caulobacter crescentus, the HHK ShkA is essential for accurate timing of the G1-S cell cycle transition and is regulated by the corresponding increase in the level of the second messenger c-di-GMP. Here, we use a combination of X-ray crystallography, NMR spectroscopy, functional analyses, and kinetic modeling to reveal the regulatory mechanism of ShkA. In the absence of c-di-GMP, ShkA predominantly adopts a compact domain arrangement that is catalytically inactive. C-di-GMP binds to the dedicated pseudoreceiver domain Rec1, thereby liberating the canonical Rec2 domain from its central position where it obstructs the large-scale motions required for catalysis. Thus, c-di-GMP cannot only stabilize domain interactions, but also engage in domain dissociation to allosterically invoke a downstream effect. Enzyme kinetics data are consistent with conformational selection of the ensemble of active domain constellations by the ligand and show that autophosphorylation is a reversible process.

Keywords: autophosphorylation; c-di-GMP; hybrid histidine kinase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Caulobacter crescentus / genetics
  • Caulobacter crescentus / metabolism*
  • Cell Cycle / physiology
  • Crystallography, X-Ray
  • Cyclic GMP / analogs & derivatives*
  • Cyclic GMP / chemistry
  • Cyclic GMP / metabolism
  • Histidine Kinase / chemistry*
  • Histidine Kinase / genetics
  • Histidine Kinase / metabolism*
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Phosphorylation
  • Protein Binding
  • Protein Conformation
  • Protein Domains
  • Second Messenger Systems


  • Bacterial Proteins
  • bis(3',5')-cyclic diguanylic acid
  • Histidine Kinase
  • Cyclic GMP

Associated data

  • PDB/6QRJ
  • PDB/6QRL