Thiazolium C(2)-proton exchange: general-base catalysis, direct proton transfer, and acid inhibition

1989 ◽  
Vol 111 (2) ◽  
pp. 674-683 ◽  
Author(s):  
Michael W. Washabaugh ◽  
William P. Jencks
Keyword(s):  
Proton Transfer ◽  
Proton Exchange ◽  
Acid Inhibition ◽  
Base Catalysis ◽  
General Base

The oxidation of aldehydes with bromine. II. Study of the general base catalysis

1964 ◽  
Vol 17 (11) ◽  
pp. 1210 ◽  
Author(s):  
BG Cox ◽  
PT McTigue
Keyword(s):  
Proton Transfer ◽  
Carboxylic Acids ◽  
Base Catalysis ◽  
Aliphatic Aldehydes ◽  
General Base

It is shown that the oxidation with bromine of four aliphatic aldehydes to the corresponding carboxylic acids involves a rate-determining proton transfer. It is concluded that the aldehyde hydrate is the reactive entity in these oxidations.

FRUCTOSE DIPHOSPHATE ALDOLASE FROM FUSARIUM OXYSPORUM f. LYCOPERSICI: III. STUDIES ON THE MECHANISM OF REACTION

1967 ◽  
Vol 45 (12) ◽  
pp. 1909-1917 ◽  
Author(s):  
J. M. Ingram
Keyword(s):  
Fusarium Oxysporum ◽  
Proton Exchange ◽  
Base Catalysis ◽  
Dihydroxyacetone Phosphate ◽  
Amino Acid Residues ◽  
Cleavage Rate ◽  
General Base ◽  
Mechanism Of Reaction ◽  
Cleavage Reactions ◽  
Rate Limiting

Frnctose-1,6-diphosphate aldolase from Fusarium oxysporum f. lycopersici is inhibited by acetylimidazole. The inhibition is reduced in the presence of fructose diphosphate or DL-glyceraldehyde-3-phosphate, but not in the presence of dihydroxyacetone phosphate. Under conditions of almost total inactivation, as measured by the rate of cleavage of fructose diphosphate, the decrease in the rate of exchange is only 18%. These results indicate that the amino acid residues which are altered under these conditions are concerned with the D-glyceraldehyde-3-phosphate rather than the dihydroxyacetone phosphate active site.The rate of cleavage of fructose diphosphate in D2O decreases, with increasing pH, more rapidly than the rate in H2O and resembles the decreased rate of tritium exchange into dihydroxyacetone phosphate with increasing pH. These results suggest that a correlation exists between the isolated proton exchange and cleavage reactions and that the decreased rate of exchange and cleavage with increasing pH is due to a decreased rate of proton neutralization of the enzyme – dihydroxyacetone phosphate anion. The addition of acetaldehyde to the aldolase assays at pH 8.0 and pH 9.0 stimulates the cleavage rate of fructose diphosphate to a level normally obtained at pH 7.5, confirming the supposition that the release of dihydroxyacetone phosphate becomes rate limiting with increasing pH. The results obtained by following the cleavage in D2O also indicate that general base catalysis is involved in the proton neutralization step and that the pK of the general base is less than pH 6.0. The evidence suggests that the general base is either a β-COOH of aspartate or a γ-COOH of glutamate.

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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