Ricin A-chain: kinetics, mechanism, and RNA stem-loop inhibitors.
Ricin A-chain (RTA) catalyzes the depurination of a single adenine at position 4324 of 28S rRNA in a N-ribohydrolase reaction. The mechanism and specificity for RTA are examined using RNA stem-loop structures of 10-18 nucleotides which contain the required substrate motif, a GAGA tetraloop. At the optimal pH near 4.0, the preferred substrate is a 14-base stem-loop RNA which is hydrolyzed at 219 min-1 with a kcat/Km of 4.5 x 10(5) M-1 s-1 under conditions of steady-state catalysis. Smaller or larger stem-loop RNAs have lower kcat values, but all have Km values of approximately 5 microM. Both the 10- and 18-base substrates have kcat/Km near 10(4) M-1 s-1. Covalent cross-linking of the stem has a small effect on the kinetic parameters. Stem-loop DNA (10 bases) of the same sequence is also a substrate with a kcat/Km of 0.1 that for RNA. Chemical mechanisms for enzymatic RNA depurination reactions include leaving group activation, stabilization of a ribooxocarbenium transition state, a covalent enzyme-ribosyl intermediate, and ionization of the 2'-hydroxyl. A stem-loop RNA with p-nitrophenyl O-riboside at the depurination site is not a substrate, but binds tightly to the enzyme (Ki = 0.34 microM), consistent with a catalytic mechanism of leaving group activation. The substrate activity of stem-loop DNA eliminates ionization of the 2'-hydroxyl as a mechanism. Incorporation of the C-riboside formycin A at the depurination site provides an increased pKa of the adenine analogue at N7. Binding of this analogue (Ki = 9.4 microM) is weaker than substrate which indicates that the altered pKa at this position is not an important feature of transition state recognition. Stem-loop RNA with phenyliminoribitol at the depurination site increases the affinity substantially (Ki = 0.18 microM). The results are consistent with catalysis occurring by leaving group protonation at ring position(s) other than N7 leading to a ribooxocarbenium ion transition state. Small stem-loop RNAs have been identified with substrate activity within an order of magnitude of that reported for intact ribosomes.
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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D004791:Enzyme Inhibitors / Q000138:chemical synthesis / Q000494:pharmacology; D005573:Formycins / Q000494:pharmacology; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D009699:N-Glycosyl Hydrolases / Q000037:antagonists & inhibitors; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000494:pharmacology; D009943:Organophosphorus Compounds / Q000494:pharmacology; D018749:RNA, Plant / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D012339:RNA, Ribosomal, 28S / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D012255:Ribitol / Q000031:analogs & derivatives / Q000494:pharmacology; D012276:Ricin / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity
D004791:Enzyme Inhibitors; D005573:Formycins; D009843:Oligoribonucleotides; D009943:Organophosphorus Compounds; D018749:RNA, Plant; D012339:RNA, Ribosomal, 28S; C089322:phenyliminoribitol; D012255:Ribitol; C034550:formycin; D012276:Ricin; D009699:N-Glycosyl Hydrolases