Structural Biochemistry of a Bacterial Checkpoint Protein Reveals Diadenylate Cyclase Activity Regulated by DNA Recombination Intermediates

Mol Cell. 2008 Apr 25;30(2):167-78. doi: 10.1016/j.molcel.2008.02.020.

Abstract

To reveal mechanisms of DNA damage checkpoint initiation, we structurally and biochemically analyzed DisA, a protein that controls a Bacillus subtilis sporulation checkpoint in response to DNA double-strand breaks. We find that DisA forms a large octamer that consists of an array of an uncharacterized type of nucleotide-binding domain along with two DNA-binding regions related to the Holliday junction recognition protein RuvA. Remarkably, the nucleotide-binding domains possess diadenylate cyclase activity. The resulting cyclic diadenosine phosphate, c-di-AMP, is reminiscent but distinct from c-di-GMP, an emerging prokaryotic regulator of complex cellular processes. Diadenylate cyclase activity is unaffected by linear DNA or DNA ends but strongly suppressed by branched nucleic acids such as Holliday junctions. Our data indicate that DisA signals DNA structures that interfere with chromosome segregation via c-di-AMP. Identification of the diadenylate cyclase domain in other eubacterial and archaeal proteins implies a more general role for c-di-AMP in prokaryotes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacillus subtilis / enzymology*
  • Bacillus subtilis / genetics
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Cell Cycle Proteins / chemistry*
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Crystallography, X-Ray
  • DNA Breaks, Double-Stranded*
  • DNA, Cruciform / chemistry
  • DNA, Cruciform / metabolism
  • Dinucleoside Phosphates / chemistry
  • Dinucleoside Phosphates / metabolism
  • Molecular Sequence Data
  • Phosphorus-Oxygen Lyases / chemistry*
  • Phosphorus-Oxygen Lyases / genetics
  • Phosphorus-Oxygen Lyases / metabolism
  • Protein Structure, Tertiary
  • Recombination, Genetic
  • Solutions
  • Spores, Bacterial / enzymology
  • Spores, Bacterial / genetics
  • Thermotoga maritima / enzymology*
  • Thermotoga maritima / genetics

Substances

  • Bacterial Proteins
  • Cell Cycle Proteins
  • DNA, Cruciform
  • Dinucleoside Phosphates
  • Solutions
  • cyclic diadenosine phosphate
  • Phosphorus-Oxygen Lyases
  • diadenylate cyclase, Bacillus subtilis

Associated data

  • PDB/3C1Y
  • PDB/3C1Z
  • PDB/3C21
  • PDB/3C23