Probing General Base Catalysis in the Hammerhead Ribozyme

2008 ◽  
Vol 130 (46) ◽  
pp. 15467-15475 ◽  
Author(s):  
Jason M. Thomas ◽  
David M. Perrin
Keyword(s):  
Hammerhead Ribozyme ◽  
Base Catalysis ◽  
General Base

scholarly journals Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis

PLoS Biology ◽  
2008 ◽  
Vol 6 (9) ◽  
pp. e234 ◽  
Author(s):  
Young-In Chi ◽  
Monika Martick ◽  
Monica Lares ◽  
Rosalind Kim ◽  
William G Scott ◽  
...  
Keyword(s):  
Hammerhead Ribozyme ◽  
Base Catalysis ◽  
General Base

scholarly journals Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid–base catalysis

2014 ◽  
Vol 70 (9) ◽  
pp. 2256-2263 ◽  
Author(s):  
Eric P. Schultz ◽  
Ernesto E. Vasquez ◽  
William G. Scott
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
Hammerhead Ribozyme ◽  
Base Catalysis ◽  
Metal Ion Binding ◽  
Acid Base ◽  
Kinetic Measurements ◽  
Structural Role ◽  
General Base

The hammerhead ribozyme catalyzes RNA cleavageviaacid–base catalysis. Whether it does so by general acid–base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid–base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme fromSchistosoma mansoniwith a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pKaof the substituted purine; in both cases inosine, which is similar to G in pKaand hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data.

scholarly journals Capturing hammerhead ribozyme structures in action by modulating the rate of general base catalysis

2008 ◽  
Vol 64 (a1) ◽  
pp. C156-C156
Author(s):  
Y.-I. Chi ◽  
M. Martick ◽  
R. Kim ◽  
W.G. Scott ◽  
S.-H. Kim
Keyword(s):  
Hammerhead Ribozyme ◽  
Base Catalysis ◽  
General Base

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.

Micellar catalysis of organic reactions. VIII. Kinetic studies of the hydrolysis of 2-acetyloxybenzoic acid (aspirin) in the presence of micelles

1982 ◽  
Vol 35 (7) ◽  
pp. 1357 ◽  
Author(s):  
TJ Broxton
Keyword(s):  
Aqueous Solution ◽  
Cetyltrimethylammonium Bromide ◽  
Cetylpyridinium Chloride ◽  
Kinetic Studies ◽  
Base Catalysis ◽  
Plateau Region ◽  
General Base ◽  
Mechanism Of Hydrolysis ◽  
Ph Range ◽  
Hydrolysis Of

The hydrolysis of 2-acetyloxybenzoic acid in the pH range 6-12 has been studied in the presence of micelles of cetyltrimethylammonium bromide (ctab) and cetylpyridinium chloride (cpc). In the plateau region (pH 6-8) the hydrolysis is inhibited by the presence of micelles, while in the region where the normal BAC2 hydrolysis (pH > 9) occurs the reaction is catalysed by micelles of ctab and cpc. The mechanism of hydrolysis in the plateau region is shown to involve general base catalysis by the adjacent ionized carboxy group both in the presence and absence of micelles. This reaction is inhibited in the presence of micelles because the substrate molecules are solubilized into the micelle and water is less available in this environment than in normal aqueous solution.

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