Proton-relay mechanism

In the 3D structure of GatCAB solved at 2.3 A of resolution, the glutaminase active center and the binding site of the CCA end of tRNA are 30 A apart. The two sites are connected by a channel, mostly hydrophobic in the outside, but lined inside with a succession of alternating strictly conserved positive and negative residues. The structure suggests a proton relay mechanism that carries ammonia from one site to the other by repeated... 

The proton-relay mechanism anchors the substrate by 3-point docking. 

Figure 6. (A) The proton relay network of the actinohodin KR active site. (B) The proposed proton-relay mechanism and the three-point docking of the substrate.

The conserved active-site residues, His-48 and Asp-99 (pancreatic enzyme numbering), provide the catalytic dyad and, with the availability of the crystal structure of the pancreatic enzyme, have been shown to produce the proton-relay mechanism (Fig. 5) [17]. In this mechanism, a water molecule acts instead of the serine found in the classical protease/lipase catalytic triad mechanisms. More recently, an alternative mechanism of catalysis has been proposed that involves two water molecules (W5 and W6) seen at the active site of the crystal structure (Fig. 6). In this mechanism, proposed by Jain (J. Rogers,... 

Fig. 5. Proton-relay mechanism of hydrolysis proposed by Verheij for secreted phospholipases Aj [17].

Fig. 6.9 Water mediation in catalysis (I). In the action of this DNA polymerase, the initial proton transfer to the a-phosphate of the substrate via a bridging crystal water molecule is the rate-limiting step. Subsequently, departure of the pyrophosphate is facilitated by a proton relay mechanism through mediation of water, which neutralizes the evolving negative charge. (Reprinted with permission from Ref. [67], 2007 American Chemical Society.)...

FIGURE 7.2. Two alternative mechanisms for the catalytic reaction of serine proteases. Route a corresponds to the electrostatic catalysis mechanism while route b corresponds to the double proton transfer (or the charge relay mechanism), gs ts and ti denote ground state, transition state and tetrahedral intermediate, respectively. 

Double proton transfer mechanism, see Serine proteases, charge-relay mechanism... 

CHj)3C.CO.OE, by attack of the serine hydroxyl group on the carbonyl carbon atom of 4-nitrophenyl trimethylacetate. This attack is assisted by proton removal from the hydroxyl group by the charge-relay mechanism, Scheme 13. It is also considered that breakdown of trimethylacetylchymo-trypsin may be assisted by the charge-relay mechanism. In this case, a proton... 

Dworschack and Plapp presented a mechanism based on this proton relay system and this is shown in Scheme The alcohol or carbonyl groups are bonded to the zinc, as is the water molecule, giving a five-coordinate zinc. 

FIGURE 3. Possible relay mechanism in the protonation of an enol... 

This enzyme, which is relatively stable under reaction conditions, will retain 70% of its activity after 10 days at pH 5 and 25°C. Although it is not yet commercially available, it has been overexpressed in E. coli, making large quantities easily accessible.68 The detailed mechanism of DERA has been determined based on the atomic structure (ca. 1.0 A) combined with site-directed mutagenesis, kinetic, and NMR studies136 (Scheme 5Alb). A proton relay system composed of Lys and Asp appears to activate a conserved active-site water that functions as the critical mediator for proton transfer in acid-base catalysis. 

Cunane, L. M., Chen, Z.-w., Shamala, N., Mathews, F. S., Cronin, C. N., and Mclntire, W. S., 2000, Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex gated substrate entry and proton relays support the proposed catalytic mechanism. J. Mol. Biol. 295 357n374. 

In another case, 1 was used to deprotect the 2-(allyloxy)phenylacetyl group, employed as a protecting functionality in carbohydrate chemistry242. Thus, heating compound 266 with a palladium catalyst/proton sponge system results in an almost quantitative yield of compound 268 (equation 29). In accordance with a postulated relay mechanism, the phenolic allyl ether is cleaved by the transition metal followed by intramolecular ester cleavage by nucleophilic attack of the released hydroxyl. The aforementioned conditions... 

Scheme 7. Possible examples of the anionic leaving-group acting as the ultimate proton acceptor in either a SNi type mechanism that leads to retention of configuration or, in a reaction mixture that contains exchangeable protons (SH), via a Sn2 -like mechanism involving a proton relay. The former is plausible for cases where X = triflate or similar very good leaving groups that can spontaneously ionize, whereas the...

The proposed catalytic mechanism involves a proton relay-type reaction where an immobilized HjO molecule serves as the nucleophile, a role normally filled by serine. The proton relay system is buried in the hydrophobic active-site wall. Ca " " binds the phosphate moiety of the substrate and, serving as a Lewis acid, polarizes the ester bond at the carbonyl oxygen. The HjO molecule, immobilized by the Asp-His pair attacks the carbonyl of the substrate and donates an H" " to His. The alkoxy oxygen of the glycerol backbone then retrieves the H" " from the His to complete the reaction. 

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