Pyridoxal 5′-phosphate: electrophilic catalyst extraordinaire

Abstract

Studies of nonenzymatic electrophilic catalysis of carbon deprotonation of glycine show that pyridoxal 5'-phosphate (PLP) strongly enhances the carbon acidity of α-amino acids, but that this is not the overriding mechanistic imperative for cofactor catalysis. Although the fully protonated PLP-glycine iminium ion adduct exhibits an extraordinary low α-imino carbon acidity (pKa = 6), the more weakly acidic zwitterionic iminium ion adduct (pKa = 17) is selected for use in enzymatic reactions. The similar α-imino carbon acidities of the iminium ion adducts of glycine with 5'-deoxypyridoxal and with phenylglyoxylate shows that the cofactor pyridine nitrogen plays a relatively minor role in carbanion stabilization. The 5'-phosphodianion group of PLP likely plays an important role in catalysis by providing up to 12 kcal/mol of binding energy that may be utilized for transition state stabilization.

NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity

“…While traditional views of PLP catalysis maintain the need for a protonated pyridine nitrogen to stabilize the buildup of negative charge generated during the reaction, more recent experimental 33,99−101 and theoretical 25,27,102,103 considerations point to a trade-off between the maximum electrophilic strength offered by a true quinonoid intermediate and reaction specificity that may be conferred by alternative protonation states. 26 In the case of the TS quinonoid intermediate, E(Q 3 ), the next step in catalysis requires protonation at the substrate C α (Scheme 3). This proton is presumably supplied by the positively charged ε-amino group of βLys87, which is positioned nearly equidistant between the cofactor C4′ and substrate C α .…”

“…These partial charge calculations help to place the TS 2AP protonation states in context: although the PLP cofactor in TS is expected to be less electrophilic due to the deprotonated pyridine ring nitrogen, it appears that this is an important component in maintaining reaction specificity by giving a more C α -localized carbanionic species. 7,26 …”

“…7,23−25 Several groups have put forward the hypothesis that in certain cases the intermediate that forms is not a true quinonoid, but rather a carbanionic species—the chief distinction again being whether the pyridine ring nitrogen is protonated and can thus support significant quinone character. 7,26−28 This hypothesis is supported by structural studies of several PLP-dependent enzymes that find hydrogen-bonding interactions between the pyridine ring nitrogen and side chains of polar, nonacidic residues, such as serine, and positively charged residues, such as arginine. 29−32 These side chains are not logical proton donors for conversion to the canonical quinonoid structure.…”

Computation of kinetic isotope effects for enzymatic reactions

“…This equilibrium plays a role that affects the reactivity of the PLP Schiff base in the active site. Richard and coworkers suggested that PLP-dependent enzymes select the zwitterionic external aldimine complex, in which pronation at the imine nitrogen is preferred [60, 61]. …”

Crystal Structure of Citrobacter freundii Asp214Ala Tyrosine Phenollyase Reveals that Asp214 is Critical for Maintaining a Strain in the Internal Aldimine

“…5 In most cases, the role of PLP is stabilization of the formed carbanionic quinonoid intermediate by delocalization of its negative charge through extensive conjugation of the π-electrons in the aldimine bond, pyridine ring and phenolate group (deprotonated O3′ atom) of PLP. 6 The protonated form of the pyridine N1 atom is stabilized by the nearby negatively charged (Asp, Glu) or neutral side chains (Ser, Thr) in a saltbridge and/or hydrogen-bond interaction. In PLPdependent enzymes for which destabilization of the quinonoid intermediate actually enhances the enzymatic reaction, a positively charged residue (e.g.…”