Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition

Structure. 2007 Aug;15(8):915-27. doi: 10.1016/j.str.2007.06.016.


Cyclic di-guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial second messenger involved in the regulation of cell surface-associated traits and persistence. We have determined the crystal structure of PleD from Caulobacter crescentus, a response regulator with a diguanylate cyclase (DGC) domain, in its activated form. The BeF(3)(-) modification of its receiver domain causes rearrangement with respect to an adaptor domain, which, in turn, promotes dimer formation, allowing for the efficient encounter of two symmetric catalytic domains. The substrate analog GTPalphaS and two putative cations are bound to the active sites in a manner similar to adenylate cyclases, suggesting an analogous two-metal catalytic mechanism. An allosteric c-di-GMP-binding mode that crosslinks DGC and an adaptor domain had been identified before. Here, a second mode is observed that crosslinks the DGC domains within a PleD dimer. Both modes cause noncompetitive product inhibition by domain immobilization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allosteric Regulation
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Catalysis
  • Catalytic Domain
  • Caulobacter crescentus / enzymology
  • Crystallography, X-Ray
  • Dimerization
  • Dose-Response Relationship, Drug
  • Enzyme Activation
  • Escherichia coli Proteins
  • Feedback, Physiological / physiology*
  • Guanosine Triphosphate / pharmacology
  • Inhibitory Concentration 50
  • Kinetics
  • Models, Biological
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Phosphorus-Oxygen Lyases / analysis
  • Phosphorus-Oxygen Lyases / chemistry*
  • Phosphorus-Oxygen Lyases / metabolism
  • Phosphorylation
  • Protein Binding
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Second Messenger Systems*


  • Bacterial Proteins
  • Escherichia coli Proteins
  • PleD protein, Caulobacter crescentus
  • Guanosine Triphosphate
  • Phosphorus-Oxygen Lyases
  • diguanylate cyclase

Associated data

  • PDB/2V0N