title: Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems.
abstract: Current genetic and molecular evidence places all the known type I restriction and modification systems of Escherichia coli and Salmonella enterica into one of four discrete families: type IA, IB, IC or ID. StySBLI is the founder member of the ID family. Similarities of coding sequences have identified restriction systems in E.coli and Klebsiella pneumoniae as probable members of the type ID family. We present complementation tests that confirm the allocation of EcoR9I and KpnAI to the ID family. An alignment of the amino acid sequences of the HsdS subunits of StySBLI and EcoR9I identify two variable regions, each predicted to be a target recognition domain (TRD). Consistent with two TRDs, StySBLI was shown to recognise a bipartite target sequence, but one in which the adenine residues that are the substrates for methylation are separated by only 6 bp. Implications of family relationships are discussed and evidence is presented that extends the family affiliations identified in enteric bacteria to a wide range of other genera.
authors.affiliation: Institute of Cell and Molecular Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK.
authors.forename: A J
authors.initials: AJ
authors.lastname: Titheradge
authors.forename: J
authors.initials: J
authors.lastname: King
authors.forename: J
authors.initials: J
authors.lastname: Ryu
authors.forename: N E
authors.initials: NE
authors.lastname: Murray
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D015280:DNA Restriction-Modification Enzymes / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis; D015253:Deoxyribonucleases, Type I Site-Specific / Q000145:classification* / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology*; D005816:Genetic Complementation Test; D007711:Klebsiella pneumoniae / Q000201:enzymology*; D008969:Molecular Sequence Data; D021122:Protein Subunits; D019779:Salmonella enterica / Q000201:enzymology; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial; C113046:HSDS protein, Bacteria; D021122:Protein Subunits; C438598:endodeoxyribonuclease EcoR9I; C438599:endodeoxyribonuclease StySBLI; D015253:Deoxyribonucleases, Type I Site-Specific