General base catalysis in nucleophilic attack at sp3 carbon of methylase model compounds

1976 ◽  
Vol 98 (4) ◽  
pp. 1057-1059 ◽  
Author(s):  
James K. Coward ◽  
Roger Lok ◽  
Orinne Takagi
Keyword(s):  
Base Catalysis ◽  
Nucleophilic Attack ◽  
Model Compounds ◽  
General Base

scholarly journals Classification of the nucleolytic ribozymes based upon catalytic mechanism

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1462
Author(s):  
David M.J. Lilley
Keyword(s):  
Catalytic Mechanism ◽  
Base Catalysis ◽  
Nucleophilic Attack ◽  
Rna Cleavage ◽  
Hydroxyl Groups ◽  
Acid Base ◽  
General Base ◽  
Cleavage Reactions ◽  
Mechanistic Basis

The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2′-oxygen atom on the adjacent phosphorus with an acceleration of a million-fold or greater. A major part of this arises from concerted general acid–base catalysis. Recent identification of new ribozymes has expanded the group to a total of nine and this provides a new opportunity to identify sub-groupings according to the nature of the general base and acid. These include nucleobases, hydrated metal ions, and 2′-hydroxyl groups. Evolution has selected a number of different combinations of these elements that lead to efficient catalysis. These differences provide a new mechanistic basis for classifying these ribozymes.

scholarly journals Mechanisms of RNA catalysis

2011 ◽  
Vol 366 (1580) ◽  
pp. 2910-2917 ◽  
Author(s):  
David M. J. Lilley
Keyword(s):  
Distinct Species ◽  
Base Catalysis ◽  
Nucleophilic Attack ◽  
Phosphoryl Transfer ◽  
Rna Catalysis ◽  
Rna Molecules ◽  
General Base ◽  
General Acid ◽  
Guanine And Adenine ◽  
Self Splicing

Ribozymes are RNA molecules that act as chemical catalysts. In contemporary cells, most known ribozymes carry out phosphoryl transfer reactions. The nucleolytic ribozymes comprise a class of five structurally-distinct species that bring about site-specific cleavage by nucleophilic attack of the 2′-O on the adjacent 3′-P to form a cyclic 2′,3′-phosphate. In general, they will also catalyse the reverse reaction. As a class, all these ribozymes appear to use general acid–base catalysis to accelerate these reactions by about a million-fold. In the Varkud satellite ribozyme, we have shown that the cleavage reaction is catalysed by guanine and adenine nucleobases acting as general base and acid, respectively. The hairpin ribozyme most probably uses a closely similar mechanism. Guanine nucleobases appear to be a common choice of general base, but the general acid is more variable. By contrast, the larger ribozymes such as the self-splicing introns and RNase P act as metalloenzymes.

Kinetics of cyclization of S-ethoxycarbonylmethylisothiouronium chloride to 2-imino-4-thiazolidone

1979 ◽  
Vol 44 (3) ◽  
pp. 912-917 ◽  
Author(s):  
Vladimír Macháček ◽  
Said A. El-bahai ◽  
Vojeslav Štěrba
Keyword(s):  
Hydrochloric Acid ◽  
Dilute Hydrochloric Acid ◽  
Base Catalysis ◽  
General Base ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Kinetics Of Formation ◽  
Acid Catalyzed ◽  
Rate Limiting ◽  
Kinetics Of

Kinetics of formation of 2-imino-4-thiazolidone from S-ethoxycarbonylmethylisothiouronium chloride has been studied in aqueous buffers and dilute hydrochloric acid. The reaction is subject to general base catalysis, the β value being 0.65. Its rate limiting step consists in acid-catalyzed splitting off of ethoxide ion from dipolar tetrahedral intermediate. At pH < 2 formation of this intermediate becomes rate-limiting; rate constant of its formation is 2 . 104 s-1.

Evidence for general base catalysis by protic solvents in a kinetic study of alcoholyses and hydrolyses of 1-(phenoxycarbonyl)pyridinium ions under both solvolytic and non-solvolytic conditions

2009 ◽  
Vol 74 (1) ◽  
pp. 43-55 ◽  
Author(s):  
Dennis N. Kevill ◽  
Byoung-Chun Park ◽  
Jin Burm Kyong
Keyword(s):  
Second Order ◽  
Base Catalysis ◽  
Substitution Reactions ◽  
Third Order ◽  
Methoxy Derivative ◽  
First Order ◽  
General Base ◽  
Protic Solvents ◽  
Kinetics Of ◽  
Pyridinium Ions

The kinetics of nucleophilic substitution reactions of 1-(phenoxycarbonyl)pyridinium ions, prepared with the essentially non-nucleophilic/non-basic fluoroborate as the counterion, have been studied using up to 1.60 M methanol in acetonitrile as solvent and under solvolytic conditions in 2,2,2-trifluoroethan-1-ol (TFE) and its mixtures with water. Under the non- solvolytic conditions, the parent and three pyridine-ring-substituted derivatives were studied. Both second-order (first-order in methanol) and third-order (second-order in methanol) kinetic contributions were observed. In the solvolysis studies, since solvent ionizing power values were almost constant over the range of aqueous TFE studied, a Grunwald–Winstein equation treatment of the specific rates of solvolysis for the parent and the 4-methoxy derivative could be carried out in terms of variations in solvent nucleophilicity, and an appreciable sensitivity to changes in solvent nucleophilicity was found.

scholarly journals Structure of a canonical RNase YoeB bound to the ribosome

2014 ◽  
Vol 70 (a1) ◽  
pp. C207-C207
Author(s):  
Yun Chen ◽  
Shu Feng ◽  
Katsuhiko Kamada ◽  
Han Wang ◽  
Kai Tang ◽  
...  
Keyword(s):  
Specific Activity ◽  
Base Catalysis ◽  
Mass Spectrometry Data ◽  
Catalytic Core ◽  
General Base ◽  
Rna Hydrolysis ◽  
70S Ribosome ◽  
A Site ◽  
Insight Into

As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3'–phosphate at the newly formed 3' end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity.

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