title: Evolutionary relationship between different subgroups of restriction endonucleases.
abstract: The type II restriction endonuclease SsoII shows sequence similarity with 10 other restriction endonucleases, among them the type IIE restriction endonuclease EcoRII, which requires binding to an effector site for efficient DNA cleavage, and the type IIF restriction endonuclease NgoMIV, which is active as a homotetramer and cleaves DNA with two recognition sites in a concerted reaction. We show here that SsoII is an orthodox type II enzyme, which is active as a homodimer and does not require activation by binding to an effector site. Nevertheless, it shares with EcoRII and NgoMIV a very similar DNA-binding site and catalytic center as shown here by a mutational analysis, indicative of an evolutionary relationship between these three enzymes. We suggest that a similar relationship exists between other orthodox type II, type IIE, and type IIF restriction endonucleases. This may explain why similarities may be more pronounced between members of different subtypes of restriction enzymes than among the members of a given subtype.
authors.affiliation: Institut für Biochemie, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany. vera.pingoud@chemie.bio.uni-giessen.de
authors.forename: Vera
authors.initials: V
authors.lastname: Pingoud
authors.forename: Elena
authors.initials: E
authors.lastname: Kubareva
authors.forename: Gudrun
authors.initials: G
authors.lastname: Stengel
authors.forename: Peter
authors.initials: P
authors.lastname: Friedhoff
authors.forename: Janusz M
authors.initials: JM
authors.lastname: Bujnicki
authors.forename: Claus
authors.initials: C
authors.lastname: Urbanke
authors.forename: Anna
authors.initials: A
authors.lastname: Sudina
authors.forename: Alfred
authors.initials: A
authors.lastname: Pingoud
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D002850:Chromatography, Gel; D002942:Circular Dichroism; D004247:DNA / Q000378:metabolism; D004252:DNA Mutational Analysis; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000235:genetics* / Q000378:metabolism; D019281:Dimerization; D004720:Endonucleases / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D010802:Phylogeny; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014461:Ultracentrifugation
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA; D004720:Endonucleases; C045297:CCNGG-specific type II deoxyribonucleases; C046545:CCWGG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific; C413605:NgoMIV endonuclease