Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease

Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15797-802. doi: 10.1073/pnas.0507949102. Epub 2005 Oct 24.

Abstract

Among all restriction endonucleases known to date, BfiI is unique in cleaving DNA in the absence of metal ions. BfiI represents a different evolutionary lineage of restriction enzymes, as shown by its crystal structure at 1.9-A resolution. The protein consists of two structural domains. The N-terminal catalytic domain is similar to Nuc, an EDTA-resistant nuclease from the phospholipase D superfamily. The C-terminal DNA-binding domain of BfiI exhibits a beta-barrel-like structure very similar to the effector DNA-binding domain of the Mg(2+)-dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors. BfiI presumably evolved through domain fusion of a DNA-recognition element to a nonspecific nuclease akin to Nuc and elaborated a mechanism to limit DNA cleavage to a single double-strand break near the specific recognition sequence. The crystal structure suggests that the interdomain linker may act as an autoinhibitor controlling BfiI catalytic activity in the absence of a specific DNA sequence. A psi-blast search identified a BfiI homologue in a Mesorhizobium sp. BNC1 bacteria strain, a plant symbiont isolated from an EDTA-rich environment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA-Binding Proteins / chemistry
  • Deoxyribonucleases / chemistry
  • Deoxyribonucleases, Type II Site-Specific / chemistry*
  • Feedback, Physiological
  • Molecular Structure
  • Protein Conformation

Substances

  • Bacterial Proteins
  • DNA-Binding Proteins
  • Deoxyribonucleases
  • endodeoxyribonuclease BfiI
  • Deoxyribonucleases, Type II Site-Specific

Associated data

  • PDB/2C1L