Water molecules catalytic activity

Aspartic proteases are characterized by their ability to cleave peptidic substrates with the aid of two catalytically active aspartic acid residues [19]. A water molecule is activated by one Asp and attacks the scissile amide carbonyl. The other Asp donates a proton to the amide nitrogen, creating a hydrogen-bond stabilized tetrahedral intermediate, which subsequently collapses into the carboxylic acid and amine cleavage products [20,21],... 

The above-mentioned mechanism suggests that positioning the two histidines appropriately would lead to artificial ribonuclease under optimized pH conditions. Figure 6.13 shows an example of an artificial ribonuclease created in this way, which has a cyclodextrin core as the hydrophobic pocket and two histidine residues as catalytic sites. This artificial enzyme catalyzed the second step of the phosphodiester cleavage. The hydrophobic part of the cyclic phosphodiester (substrate) was accommodated into the core of the cyclodextrin and the phosphodiester was exposed between the two histidines. The water molecule was activated through proton removal (performed by the neutral histidine, left), and the activated water performed a nucleophilic attack on the phosphate atom. The protonated histidine (right) assisted this nucleophilic attack by protonating of the phosphodiester. Because of the cooperation between... 

Reactions (33) to (37) are equivalent to the overall reaction (31), which mainly occurs at higher electrode potentials (E > 0.8 V/RHE), where the water molecule is activated to form oxygenated species at the catalytic surface, whereas reaction (32) occurs mainly at lower potentials (E < 0.6 V/RHE). At intermediate potentials (0.3 < E <0.1 V/RHE), the dissociative adsorption of water occurs at plurimetallic Pt-based electrodes ... 

II. The P-loop backbone amides and the side chain of the arginine residue supplies perfect stabilization of the equatorial oxygens of the penta-coordinated transition states by a network of hydrogen bonds. III. An increased pA of the general acid/base residue results in a larger catalytic effect of the second, rate limiting step where the water molecule is activated by the general base (Oj-Xbg), compared to the first step where the same residue acts as an acid... 

The crystal structure of j-CaaD inactivated by the (if)-oxirane-2-carboxylate shows two additional active site residues (His-28 and Tyr-103) that are not present in CaaD (Figure 15(b)). ° On the basis of the interactions observed in the complex, a mechanism for air-CaaD was proposed (Figure 16). A key catalytic task for j-CaaD is to activate a water molecule. In contrast to CaaD, where the water molecule is activated by a single residue (aGlu-52), dr-CaaD uses the side chains of two residues, Glu-114 and Tyr-103, to activate the nucleophilic water molecule. The first step in catalysis is the nucleophilic attack of the activated water molecule on C-3 of r/j-3-chloroacrylate to form an enediolate intermediate. This intermediate is presumably... 

The next step involves the decarboxylation of the chain extender unit (malonyl or methylmalonyl), which is supplied by the upstream ACP. Upon binding, a water molecule is activated by one of the catalytic histidine residues, facilitating the attack at the malonyl C3 carboxylate. This releases HCOs", and the resulting eno-late is stabilised by a conserved histidine. 

En me Mechanism. Staphylococcal nuclease (SNase) accelerates the hydrolysis of phosphodiester bonds in nucleic acids (qv) some 10 -fold over the uncatalyzed rate (r93 and references therein). Mutagenesis studies in which Glu43 has been replaced by Asp or Gin have shown Glu to be important for high catalytic activity. The enzyme mechanism is thought to involve base catalysis in which Glu43 acts as a general base and activates a water molecule that attacks the phosphodiester backbone of DNA. To study this mechanistic possibiUty further, Glu was replaced by two unnatural amino acids. 

Figure 1.9 Examples of functionally important intrinsic metal atoms in proteins, (a) The di-iron center of the enzyme ribonucleotide reductase. Two iron atoms form a redox center that produces a free radical in a nearby tyrosine side chain. The iron atoms are bridged by a glutamic acid residue and a negatively charged oxygen atom called a p-oxo bridge. The coordination of the iron atoms is completed by histidine, aspartic acid, and glutamic acid side chains as well as water molecules, (b) The catalytically active zinc atom in the enzyme alcohol dehydrogenase. The zinc atom is coordinated to the protein by one histidine and two cysteine side chains. During catalysis zinc binds an alcohol molecule in a suitable position for hydride transfer to the coenzyme moiety, a nicotinamide, [(a) Adapted from P. Nordlund et al., Nature 345 593-598, 1990.)...

On the other hand, if activity decreases sharply as pH is raised, activity may depend on a protonated group, which may act as a general acid, donating a proton to the substrate or a catalytic water molecule (b). At high pH, the proton dissociates and is not available in the catalytic events. 

The structure of the aqua complex (Figure 1.51), which is an active intermediate in some catalytic systems, shows the Ru-OH2 distance to be some 0.1 A longer than in the ruthenium(III) hexaqua ion, indicating a possible reason for its lability the water molecule also lies in a fairly exposed position, away from the bulk of the EDTA group. 

On the other hand, the catalytic effect of water as a base is stronger at the 2-position. This result can be explained if one assumes that the proton is transferred by a water molecule which solvates the O- group in the reagent 3-sulfo-l-naphth-oxide dianion. As can be seen in 12.148, the base is already in the optimum position when the stage of the o-complex is reached. This explanation is supported by a comparison of the entropies of activation for reaction at the 2- and 4-positions. 

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