Leaving groups pyrophosphates

Section 26 9 Carbon-carbon bond formation between isoprene units can be understood on the basis of nucleophilic attack of the tt electrons of a double bond on a carbocation or an allyhc carbon that bears a pyrophosphate leaving group... 

Figure 13 7 The two-metal-ion mechanism for polynucleotide polymerases. One metal ion (usually Mg2+) activates the 3 -OH group of the primer terminus and stabilizes one of the partly negatively charged equatorial oxygen atoms of the phosphoryl group, whereas the other binds the phosphoryl oxygen and the oxygen atoms of the pyrophosphate leaving group. The two metal ions are 3.9 A apart. This mechanism fits both RNA and DNA polymerases. [Modified from T. A. Steitz, Nature, Lond. 391,231 (1998).]...

Show the structure of the species derived from the pyrophosphate leaving group after it has departed and explain why it is a good leaving group. 

The first step is the migration of one of the bonds (shown in green) of the three-membered ring to displace the pyrophosphate leaving group, expand the ring to four-membered, and release some strain. Now the cyclobutyl cation breaks down to give an open-chain allylic cation stabilized by one of the alkenes. This is the ca tion that is reduced by NADPH. 

Loss of the pyrophosphate leaving group forms a resonance-stabilized carbocation in Step [1], which reacts with the nucleophilic double bond of the 1° pyrophosphate to form a new C-C bond and a 3° carbocation in Step [2]. 

Figure 1 Chemical mechanism of DNA polymerase and 3 -5 exonuclease, (a) DNA polymerase reaction. The enzyme chelates two metal Ions using three aspartic acid residues (only two are shown). Metal ion A abstracts the 3 hydroxyl proton of the primer terminus to generate a nucleophile that attacks the a-phosphate of an incoming dNTP substrate. The phosphoryl transfer results In production of a pyrophosphate leaving group, which is stabilized by metal Ion B. (b) The 3 -5 exonuclease proofreading activity is located in a site that is distinct from the polymerase site yet it uses two-metal-ion chemistry similar to DNA synthesis. The reaction type is hydrolysis in which metal ion A activates water to form the hydroxy anion nucleophile. Nucleophile attack on the phosphate of the mismatched nucleotide releases it as dNMP (dGMP in the case shown).

Protein interactions with pyrophosphate leaving group Homology modeling of At4CL2 and attempted substrate-binding pocket manipulations COMTs and CCOMTs... 

Protein interactions with pyrophosphate leaving group... 

The mechanism for converting mevalonic acid into mevaionyi phosphate is essentially an Sn2 reaction with an adenosyl pyrophosphate leaving group (Section 27.3). A second Sn2 reaction converts mevaionyi phosphate to mevaionyi pyrophosphate. ATP is an excellent phosphorylating reagent for nucleophiles because its phosphoanhydride bonds are easily broken. The reason that phosphoanhydride bonds are so easily broken is discussed in Section 27.4. 

The pyrophosphate leaving group Is expelled to give a resonance-stabilized, allylic carbocation... 

The pyrophosphate leaving group is expelled to give a resonance-stabilized (allylic) carbocation. The k bond of isopentyl phosphate then functions as a nucleophile and attacks the carbocation. Finally, a basic amino acid residue of the enzyme removes a proton to give the product ... 

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