title: Mechanism of substrate recognition by the ribotoxin, alpha-sarcin.
abstract: The substrate recognition and catalytic mechanisms of alpha-sarcin were explored with kinetic method by using synthetic 25-mer RNA mimicking the alpha-sarcin/ricin loop in 23S rRNA of E. coli ribosomes. The oligomer containing deoxy-G at the site of alpha-sarcin (G14) was a potent competitive inhibitor. The RNA having deoxy-G8 however, increases the Kcat value by about five times but without significant alteration on Km. Surprisingly, the deletion of G8 makes the oligomer become a strong noncompetitive inhibitor of the enzyme. These results suggested that there are at least two sites in the RNA substrate which are recognized by alpha-sarcin, one is the G8 bulge or at around its neighbor and the other is the GAGA in the sarcin/ricin loop of the rRNA.
authors.affiliation: Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama, Japan.
authors.forename: E
authors.initials: E
authors.lastname: Takeda
authors.forename: X
authors.initials: X
authors.lastname: Bi
authors.forename: S
authors.initials: S
authors.lastname: Yoshinari
authors.forename: Y
authors.initials: Y
authors.lastname: Endo
mesh_terms: D001483:Base Sequence; D003603:Cytotoxins / Q000378:metabolism*; D003849:Deoxyguanosine; D004722:Endoribonucleases / Q000378:metabolism*; D005656:Fungal Proteins; D007700:Kinetics; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D003603:Cytotoxins; D005656:Fungal Proteins; D009843:Oligoribonucleotides; D012338:RNA, Ribosomal, 23S; C014801:alpha-sarcin; D004722:Endoribonucleases; D003849:Deoxyguanosine