Does pyridoxal 5'-phosphate function in glycogen phosphorylase as an electrophilic or a general acid catalyst?

Biochemistry ◽  
1984 ◽  
Vol 23 (24) ◽  
pp. 5853-5861 ◽  
Author(s):  
Helmut W. Klein ◽  
Mie J. Im ◽  
Dieter Palm ◽  
Ernst J. M. Helmreich
Keyword(s):  
Glycogen Phosphorylase ◽  
Acid Catalyst ◽  
General Acid

scholarly journals Arginine as a General Acid Catalyst in Serine Recombinase-mediated DNA Cleavage

2013 ◽  
Vol 288 (40) ◽  
pp. 29206-29214 ◽  
Author(s):  
Ross A. Keenholtz ◽  
Kent W. Mouw ◽  
Martin R. Boocock ◽  
Nan-Sheng Li ◽  
Joseph A. Piccirilli ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Acid Catalyst ◽  
Serine Recombinase ◽  
General Acid

The mechanism of the nonenzymatic iodination of tyrosine by molecular iodine

1988 ◽  
Vol 66 (9) ◽  
pp. 967-978 ◽  
Author(s):  
H. Brian Dunford ◽  
Adejare J. Adeniran
Keyword(s):  
Ph Dependence ◽  
Acid Catalyst ◽  
Order Rate Constant ◽  
Molecular Iodine ◽  
Base Catalysis ◽  
Slow Step ◽  
Rate Law ◽  
General Acid ◽  
Phenolic Group ◽  
Ph Range

Over the pH range 7–10, at very low buffer concentration, the nonenzymatic iodination of tyrosine obeys the rate law[Formula: see text]where kapp is the measured second order rate constant based upon the total initial concentrations of molecular iodine and tyrosine and K2 (units M) is the equilibrium constant for [Formula: see text]. The value of k′ is 3.5 × 10−8 M∙s−1. There are three plausible mechanisms that fit the experimental data. One, the simplest, is a concerted process in which hypoiodous acid attacks tyrosine with its phenolic group unionized. The other two involve the formation of an iodinated quinoid reactive intermediate species in a rapid pre-equilibrium between unionized tyrosine and either hypoiodous acid or molecular iodine. The pre-equilibrium, if it occurs, favors the initial reactants. It is followed by a slow step in which the quinoid is converted to mono-iodinated tyrosine. Positive deviations from the rate law for pH dependence indicate that some specific acid catalysis (H3O+) is occurring in the pH range 5–7. In the presence of sufficient buffer, general acid–base catalysis is observed with acetic acid acting as a general acid catalyst in the vicinity of pH 5 and carbonate acting as a general base at pH ~ 9.5. The nonenzymatic iodination of tyrosine occurs more rapidly as the pH is increased, in marked contrast to the peroxidase-catalyzed iodination, which has its optimum at low pH.

Solvent effects on kinetics and mechanism of acid-catalyzed decomposition of 1,3-bis(4-methylphenyl)triazene I. Reactions in alcohols

1990 ◽  
Vol 55 (1) ◽  
pp. 147-155 ◽  
Author(s):  
Taťjana Nevěčná ◽  
Oldřich Pytela ◽  
Miroslav Ludwig ◽  
Jaromír Kaválek
Keyword(s):  
Trichloroacetic Acid ◽  
Acid Catalysis ◽  
Acid Catalyst ◽  
Kinetics And Mechanism ◽  
Acid Catalysts ◽  
Effect Of Solvents ◽  
Protic Solvents ◽  
General Acid ◽  
Catalytically Active ◽  
Acid Catalyzed

The effect of protic solvents (methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 2-butanol, cyclohexanol) has been studied on the kinetics and mechanism of acid-catalyzed decomposition of 1,3-bis(4-methylphenyl)triazene, using trichloroacetic acid as the acid catalyst. Both the non-dissociated acid and the proton have been found to be catalytically active. The mechanism of splitting of the triazene substrate with the non-dissociated acid involves the general acid catalysis. Comparison of the catalytic rate constants of the two acid catalysts and effect of solvents on these values indicate that the general acid catalysis probably also operates in the reaction of the substrate with proton.

scholarly journals Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

2015 ◽  
Vol 112 (40) ◽  
pp. 12384-12389 ◽  
Author(s):  
Qun Wan ◽  
Jerry M. Parks ◽  
B. Leif Hanson ◽  
Suzanne Zoe Fisher ◽  
Andreas Ostermann ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Bound States ◽  
Direct Determination ◽  
Acid Catalyst ◽  
Active Site Residues ◽  
General Acid ◽  
Initial Stage ◽  
Energy Simulations ◽  
Glycoside Hydrolysis ◽  
Neutron Crystallography

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.

scholarly journals Identification of general acid catalyst for the ATPase activity of Lynch syndrome-related MutL homologs

2021 ◽  
Author(s):  
Kenji Fukui ◽  
Yuki Fujii ◽  
Takato Yano
Keyword(s):  
Lynch Syndrome ◽  
Atpase Activity ◽  
Catalytic Mechanism ◽  
Ph Dependence ◽  
Acid Catalyst ◽  
Base Catalysis ◽  
Mechanism Analysis ◽  
Missense Mutations ◽  
Aquifex Aeolicus ◽  
General Acid

Mutations of mismatch repair MutL homologs are causative of a hereditary cancer, Lynch syndrome. Investigation of MutL facilitates genetic diagnoses essential for cancer risk managements and therapies. We characterized MutL homologs from human and a hyperthermophile, Aquifex aeolicus, (aqMutL) to reveal the catalytic mechanism for the ATPase activity. Although existence of a general acid catalyst had not been conceived in the mechanism, analysis of the pH dependence of the aqMutL ATPase activity revealed that the reaction is accelerated by general acid-base catalysis. Analyses of mutant aqMutLs showed that Lys79 is the general acid, and the corresponding residues were confirmed to be critical for activities of human homologs, on the basis of which a catalytic mechanism for MutL ATPase is proposed. These and other results described here would contribute to evaluating the pathogenicity of Lynch syndrome-associated missense mutations.

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