title: Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed.
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.
authors.affiliation: Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109, Warsaw, Poland. iamb@bioinfo.pl
authors.forename: J M
authors.initials: JM
authors.lastname: Bujnicki
authors.forename: M
authors.initials: M
authors.lastname: Radlinska
authors.forename: L
authors.initials: L
authors.lastname: Rychlewski
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D001665:Binding Sites; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000737:chemistry / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000378:metabolism; D019143:Evolution, Molecular; D006639:Histidine / Q000378:metabolism; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017386:Sequence Homology, Amino Acid; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D006639:Histidine; C047058:DNA modification methylase MboII; C116423:NspI methylase protein, bacteria; D004248:DNA (Cytosine-5-)-Methyltransferases; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); C048422:endodeoxyribonuclease NlaIII; C046184:endodeoxyribonuclease PaeI; C035337:CCGCGG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific; C024403:GGCC-specific type II deoxyribonucleases