Thiamin Phosphate Synthase:  The Rate of Pyrimidine Carbocation Formation

Abstract

Carbocations have fascinated organic chemists for almost a century, and the properties of this reactive intermediate have been thoroughly studied. 1 Carbocations have been proposed as intermediates in several enzyme-catalyzed reactions, such as the prenyl transfer and cyclization reactions involved in terpene biosynthesis, 2,3 the pyrrole tetramerization involved in porphyrin biosynthesis, 4 the glycosyl transfer reactions involved in a wide variety of glycosylations, 5 and, the topic of this communication, the thiazole/pyrimidine coupling reaction involved in thiamin phosphate biosynthesis. 6 This reaction, catalyzed by thiamin phosphate synthase (TP-synthase), is the penultimate step in the biosynthesis of thiamin pyrophosphate, the active form of vitamin B 1 . All organisms that synthesize thiamin pyrophosphate have some form of this coupling enzyme. Previous structural and biochemical data suggest a dissociative mechanism for TP-synthase (Scheme 1). 6-8 Here we describe a study which allowed the direct measurement of the rate constant for pyrimidine carbocation 3 formation using transient state kinetic methods.Prior to this work, the rate-limiting steps for catalysis by TPsynthase were unknown; therefore, we sought to inspect the formation of thiamin phosphate (TP) on the millisecond time scale under "burst" conditions in order to more clearly understand the kinetic pathway. As shown in Figure 1c (squares), a pre-steadystate burst of product formation was observed upon rapidly mixing TP-synthase with an excess of HMP-PP and Thz-P in a chemical quench-flow apparatus. The reaction mixture for each time point was quenched by the rapid addition of 0.25 M NaOH, and the amount of product was quantified by the oxidation of TP using K 3 Fe(CN) 6 to yield the intensely fluorescent thiochrome phosphate 7 (Figure 1b). 7 The data were fit by nonlinear regression to the following burst equation:A burst phase rate (λ) of 0.39 ( 0.02 s -1 and a steady-state phase rate (k ss /[E]) of 0.0125 ( 0.0005 s -1 were obtained. The nonzero value for [TP] in the t ) 0 time point results from a fraction of TP-synthase that co-purifies with TP. 3 If the reaction to form TP is irreversible at the active site, the amplitude (A ) 21.9 ( 0.5 µM) of the burst phase should be nearly equal to the active enzyme concentration. However, in this case, an additional level of complexity exists because the enzyme co-purifies with a fraction of product bound (both TP and PP i ). Therefore, the sum of the amplitude and the Y-intercept (C ) 5.3 ( 0.3 µM) is ∼equal to the enzyme concentration used in the burst experiment. To investigate this matter further, an active site titration was performed using the burst amplitude as a measure of active enzyme concentration. This was accomplished by taking advantage of a change in the intrinsic protein fluorescence upon addition of PP i to the TPsynthase/TP complex (see Supporting Information). The burst amplitude and the active site titration agreed well and indicated that the enzyme co-purifies with slightly l...

A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer

“…In the ligand-bound structure (‘ON’ state, right), a distinct P1 stem and a P2 stem (partial formation of the terminator) are expected to form, thereby blocking formation of the complete terminator stem and leading to transcription read-through. ( B ) Pathway for the enzymatic pyrophosphorylation of HMP using 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (ThiD), carried out as previously described (Hanes et al, 2007). ( C ) Plots of the mass-to-charge ratios (m/z) of HMP and HMP-PP prepared by enzymatic pyrophosphorylation.…”

“…Unfortunately, our use of such transcription assays was made more difficult, because HMP-PP is not commercially available and is known to be relatively unstable (Hanes et al, 2007). Therefore, we freshly generated HMP-PP from HMP and ATP enzymatically (Figure 3B) by using recombinantly produced ThiD protein.…”

A Missing Enzyme in Thiamin Thiazole Biosynthesis: Identification of TenI as a Thiazole Tautomerase

“…10,17,18 The substrate tolerance of this enzyme now becomes important in the context of TenI function. In the reconstitution of the thiazole biosynthesis described in Figure 2, cThz*-P 14 , the product of the thiazole synthase 6 is clearly a substrate for thiamin phosphate synthase.…”

Biosynthesis of Thiamin Pyrophosphate

“…The results of extensive labeling studies revealing the origins of the HMP-P atoms are shown in Fig. 12 (26, 27, 28, 29, 30, 31). …”