Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense

Structure. 2009 Jun 10;17(6):904-12. doi: 10.1016/j.str.2009.03.019.


Acquired immunity in prokaryotes is achieved by integrating short fragments of foreign nucleic acids into clustered regularly interspaced short palindromic repeats (CRISPRs). This nucleic acid-based immune system is mediated by a variable cassette of up to 45 protein families that represent distinct immune system subtypes. CRISPR-associated gene 1 (cas1) encodes the only universally conserved protein component of CRISPR immune systems, yet its function is unknown. Here we show that the Cas1 protein is a metal-dependent DNA-specific endonuclease that produces double-stranded DNA fragments of approximately 80 base pairs in length. The 2.2 A crystal structure of the Cas1 protein reveals a distinct fold and a conserved divalent metal ion-binding site. Mutation of metal ion-binding residues, chelation of metal ions, or metal-ion substitution inhibits Cas1-catalyzed DNA degradation. These results provide a foundation for understanding how Cas1 contributes to CRISPR function, perhaps as part of the machinery for processing foreign nucleic acids.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Pairing
  • Base Sequence
  • Binding Sites
  • Conserved Sequence
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • Deoxyribonucleases / chemistry*
  • Deoxyribonucleases / metabolism
  • Dimerization
  • Genome*
  • Genome, Bacterial
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Prokaryotic Cells / metabolism
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / classification*
  • Proteins / genetics*
  • Proteins / isolation & purification
  • Repetitive Sequences, Nucleic Acid / genetics*


  • DNA, Bacterial
  • Proteins
  • Deoxyribonucleases