Adjacent mechanism

So far, all evidence is consistent with the interpretation that enzymatic reactions at phosphorus proceed with inversion by an in-line associative mechanism. There has been no need to invoke adjacent mechanisms, metaphosphate intermediates, or pseudorotation. Results are summarized in Table 8.1. 

Fla. 31. Possible pathways for RNase action. The in-line mechanism is favored for step 1 by Roberts et al. (623), The adjacent mechanism requiring the intermediate step of pseudorotation is suggested by Usher (622) for step 2, the hydrolysis of the cyclic phosphate. 

The adjacent mechanism for step 1 would involve the 02 attack opposite X (or Y) and this would require protonation of X (or Y) so that it could be apical in the intermediate. Pseudorotation would then be required to allow 05" to become apical preparatory to leaving, and 03 would also become apical. Either group could then leave and specific protonation of 05" would be required to explain the lack of 2, 5"-diester formation. 

The ks curve for C > p hydrolysis is not symmetrical, and a secondary acid pathway has been proposed to explain part of the activity at pH 4.0 (499). Perhaps the protonation of both histidines produces enough polarization of the phosphate to permit direct attack by water or stabilizes the transitional state in the formation of the pentacovalent intermediate. With excess protons present, protonation of the leaving group would be easy. If histidine is not involved as a base, the ks/Km curve should also be distorted according to this view. This description would not seem to fit their model. In any case it would be interesting to see if this acid pathway is different from the normal pathway with respect to in-line vs. adjacent mechanisms. An alternate proposal is that the protonation of the acetate-tris buffer was distorting the curve. Another factor to consider is the chloride behavior as a competitive inhibitor, but this would not affect fcs if it is strictly competitive. 

In the decomposition of 0-phosphobiotin, it is most reasonable to expect that substitution will occur by an adjacent mechanism rather than by an in-line mechanism (53). The attack of bicarbonate on 0-phosphobiotin generates carboxy phosphate, which in turn can decompose to give carbon dioxide, as was discussed previously. If carbon dioxide is to be generated it must be near the N-1 position of biotin with which it must react. In the adjacent mechanism, the car-... 

Fig. 3.7. Differences between in-line and adjacent mechanism of phosphodiester bond hydrolysis, (a) First step (transesterification) in the RNase catalyzed hydrolysis of RNA illustrating two possible stereochemical pathways The in-line mechanism allows a direct displacement while the adjacent mechanism requires a pseudo-rotation, (b) Second step (hydrolysis) in the RNase catalyzed hydrolysis of RNA illustrating two possible stereochemical pathways. Again, the in-line mechanism allows a direct displacement to form the 3 -phosphate, while the adjacent mechanism requires a pseudorotation (26).

Adjacent mechanism leads to retention of configuration at phosphorus ... 

The vic-cis-6.io groups formed hydrogen bonds with the two phosphoryl oxygen atoms of the substrate so as to activate the phosphorus atoms to be attacked by nucleophiles (H2O) and the alkoxy groups to be left either by an inline or by an adjacent mechanism. In the biological system there are plenty of biopolymers containing riboses with free vic-ds-diol, which might show nuclease activities. 

The pH—activity profile of RNase A supports a mechanism that involves a diprotonic enzyme acting in a monoprotonated form. The geometry for the two-step catalysis, probed by the use of phosporothioate analogs, is consistent with an in-line rather than an adjacent mechanism (11,35-37). Kinetic studies on the cyclization of uridine 3 -P aryl esters and the effect of leaving groups suggest that electrophilicity is also involved in the catalysis (3). 

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