Protonated 2'-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme.
We have probed the electrostatic environment of the active site of the Tetrahymena group I ribozyme (E) using protonated 2'-aminoguanosine (), in which the 2'-OH of the guanosine nucleophile (G) is replaced by an group. At low concentrations of divalent metal ion (2 mM Mg(2+)), binds at least 200-fold stronger than G or G(NH)()2, with a dissociation constant of </=1 microM from the ribozyme. oligonucleotide substrate. complex (). This strong binding suggests that the group interacts with negatively charged phosphoryl groups within the active site. Increasing the concentration of divalent metal ion weakens the binding of to E. S more than 10(2)-fold. The Mn(2+) concentration dependence suggests that M(C), the metal ion that interacts with the 2'-moiety of G in the normal reaction, is responsible for this effect. M(C) and compete for binding to the active site; this competition could arise from electrostatic repulsion between the positively charged and M(C) and, possibly, from their competition for interaction with active site phosphoryl groups. The reactive phosphoryl group of S increases the competition between M(C) and, consistent with a network of interactions involving M(C) that help position the reactive phosphoryl group and the guanosine nucleophile with respect to one another. The chemical step with bound is at least 10(4)-fold slower than with G or G(NH)()2. These results provide additional support for an integral role of M(C) in catalysis by the Tetrahymena ribozyme, and demonstrate the utility of the moiety as an electrostatic probe within a structured RNA.
Shan
S O
SO
Department of Biochemistry, Stanford University, California 94305, USA.
Narlikar
G J
GJ
Herschlag
D
D
D000588:Amines; D000818:Animals; D001665:Binding Sites; D006151:Guanosine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism*; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D008345:Manganese / Q000737:chemistry / Q000378:metabolism; D008956:Models, Chemical; D009843:Oligoribonucleotides / Q000378:metabolism; D011522:Protons; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism*; D012996:Solutions; D055672:Static Electricity; D013379:Substrate Specificity; D013768:Tetrahymena / Q000201:enzymology*
D000588:Amines; C116167:GIR1 ribozyme; D009843:Oligoribonucleotides; D011522:Protons; D016337:RNA, Catalytic; D012996:Solutions; D006151:Guanosine; D008345:Manganese; D008274:Magnesium