Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed

Trends Biochem Sci. 2001 Jan;26(1):9-11. doi: 10.1016/s0968-0004(00)01690-x.

Abstract

Using algorithms for protein sequence analysis we predict that some of the canonical type II and type IIS restriction enzymes have an active site with a substantially different architecture and fold from the "typical" PD-(D/E)xK superfamily. These results suggest that they are related to nucleases from the HNH and GIY-YIG superfamilies.

MeSH terms

  • Algorithms
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Bacterial Proteins*
  • Binding Sites
  • DNA (Cytosine-5-)-Methyltransferases / chemistry
  • DNA (Cytosine-5-)-Methyltransferases / metabolism
  • Deoxyribonucleases, Type II Site-Specific / chemistry*
  • Deoxyribonucleases, Type II Site-Specific / metabolism
  • Evolution, Molecular*
  • Histidine / metabolism
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Folding*
  • Sequence Homology, Amino Acid
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / chemistry
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / metabolism

Substances

  • Bacterial Proteins
  • Histidine
  • DNA modification methylase MboII
  • NspI methylase protein, bacteria
  • DNA (Cytosine-5-)-Methyltransferases
  • Site-Specific DNA-Methyltransferase (Adenine-Specific)
  • endodeoxyribonuclease NlaIII
  • endodeoxyribonuclease PaeI
  • CCGCGG-specific type II deoxyribonucleases
  • Deoxyribonucleases, Type II Site-Specific
  • GGCC-specific type II deoxyribonucleases