Thiamin phosphate synthase: The rate of pyrimidine carbocation formation

Article abstract of DOI:10.1021/ja0679634

Thiamin phosphate synthase couples 4-amino-5-(hydroxymethyl)-2-methylpyrimidine pyrophosphate (HMP-PP) and 4-methyl-5-(β-hydroxyethyl)thiazole phosphate (Thz-P) to make thiamin phosphate on the biosynthetic route to thiamin-PP, the active form of vitamin B₁. We show that this coupling reaction goes through a pyrimidine carbocation intermediate by using transient state kinetic methods, and that the rate constant for carbocation formation at the active site of the enzyme is 0.4 s^-1. Copyright

Full text of DOI:10.1021/ja0679634

Published on Web 03/28/2007
Thiamin Phosphate Synthase: The Rate of Pyrimidine Carbocation Formation
Jeremiah W. Hanes, Steven E. Ealick,* and Tadhg P. Begley*
Department of Chemistry and Chemical Biology, Cornell UniVersity, Ithaca, New York 14853
Received November 7, 2006; E-mail: tpb2@cornell.edu; see3@cornell.edu
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 intermedi-
ates 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 glycosyl-
ations,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,
Figure 1. Pre-steady-state product formation catalyzed by TP-synthase
the active form of vitamin B1. All organisms that synthesize thiamin
using HMP-PP and two HMP-PP analogues (5 and 6). (a) The structures
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.
of the three substrates used to probe the rate of catalysis by TP-synthase
are shown. (b) The concentration of product was quantified by taking
advantage of the oxidation of TP by K3Fe(CN)6 under basic conditions to
yield the highly fluorescent compound thiochrome 7 (or thiochrome
derivatives). (c) A pre-steady-state burst of product formation was observed
upon rapidly mixing TP-synthase with an excess (500 µM) of either HMP-
PP or MeO-HMP-PP 5 and Thz-P (500 µM). (d) Shown is a single-turnover
experiment using CF3HMP-PP 6 as a substrate. The reaction was performed
under the following conditions: [TP-synthase] ) 100 µM, [CF3HMP-PP]
) 300 µM, and [Thz-P] ) 80 µM.
Scheme 1
tion. This was accomplished by taking advantage of a change in
the intrinsic protein fluorescence upon addition of PPi to the TP-
synthase/TP complex (see Supporting Information). The burst
amplitude and the active site titration agreed well and indicated
that the enzyme co-purifies with slightly less PPi than TP. It is
also important to note that both the burst rate and the burst
amplitude were independent of HMP-PP and Thz-P concentration
under all pseudo-first-order conditions examined.
Prior to this work, the rate-limiting steps for catalysis by TP-
synthase 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-steady-
state 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
K3Fe(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:
Observation of a pre-steady-state burst of product formation can
often indicate that the overall rate constant for catalysis (kcat) is
limited by product dissociation. TP-synthase is no exception as the
rate constant for the dissociation of TP nearly fully limits kcat (results
not shown). Therefore, probing the mechanism of catalysis by TP-
synthase under steady-state conditions is not informative. The
evidence at hand suggests that the observed rate of the burst phase
is largely a measure of a single irreversible step. Several possibilities
exist regarding the identity of this step and may likely be narrowed
to pyrimidine carbocation formation 3, pyrimidine carbocation
trapping by the Thz-P, or a conformational change of the protein.
To differentiate between these, the sensitivity of the burst phase
rate to carbocation stabilizing (methoxy) and destabilizing (tri-
fluoromethyl) groups was determined. If the rate of the burst phase
is limited by carbocation formation, we anticipate a large substituent
effect (i.e., methoxy . trifluoromethyl). In contrast, if the rate of
the burst phase is limited by carbocation trapping by Thz-P, we
predict a small and opposite substituent effect (i.e., methoxy <
trifluoromethyl). A conformational change is likely to be relatively
insensitive to the pyrimidine substituent (i.e., methoxy ) trifluoro-
methyl).
[Product] ) A(1 - e-λt) + ksst + C
A burst phase rate (λ) of 0.39 ( 0.02 s-1 and a steady-state phase
rate (kss/[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 PPi). 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 concentra-
Data from a burst experiment performed with MeO-HMP-PP 59
are shown in Figure 1c (circles). The observed burst phase rate
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10.1021/ja0679634 CCC: $37.00 © 2007 American Chemical Society

C O M M U N I C A T I O N S
Figure 2. Analysis of the substituent effect on the TP-synthase-catalyzed
reaction. (a) Comparison of the SN1 solvolysis of p-substituted tert-cumyl
chloride derivatives 8 to the SN2 displacement of benzyl chloride derivatives
9 and to the reaction catalyzed by TP-synthase. (b) Hammett plot (logarithm
(kobs/kMe) versus σp+) of the model SN2 displacement reactions (squares),
the model SN1 solvolysis reactions (triangles), and the enzymatic reactions
(circles). A linear fit to the enzymatic reaction data gives a F value (slope)
of -3.14 ( 0.20.
(6.2 ( 1.0 s-1) was 16 times greater than that observed for HMP-
PP. The steady-state rate also increased, although only by a factor
of about 3, and is likely due to an increase in the rate of dissociation
of methoxythiamin phosphate from the active site. The reaction
using CF3-HMP-PP 6 was extremely slow, and it was necessary to
carry out this reaction under single-turnover conditions ([TP-
synthase] > [Thz-P]) to accurately measure catalysis (Figure 1d).
The reaction proceeded to completion in a monophasic fashion and
was analyzed by fitting the data to a single-exponential equation
([Product] ) A(1-e-λt) + C) to obtain an observed rate of (3.01
( 0.23) × 10-4 s-1. The relative rates of reaction for CH3O-HMP-
Figure 3. Structure of TP-synthase with the bound pyrimidine carbocation
intermediate (PDB ID 1G67). (a) Stereoview of the active site (cross-eye
viewing). (b) Schematic representation of the key active site interactions.
3. One of the pyrophosphate oxygen atoms is located 3.03 Å from
the nitrogen of the pyrimidine amino group. This suggests that
proton transfer or hydrogen bonding of the pyrimidine amino group
to the pyrophosphate oxygen plays an important role in stabilizing
the bound carbocation.
The TP-synthase-catalyzed reaction proceeds via a carbocation
intermediate. The high stability of this intermediate, relative to that
of other enzyme-bound carbocations, makes this enzyme a uniquely
tractable experimental system. This stability has enabled us to
determine the structure of the enzyme intermediate complex and
the rate constant for carbocation formation at the active site.
PP, CH3-HMP-PP, and CF3-HMP-PP were 16, 1, and 7.7 × 10-4
,
respectively.
A Hammett plot for these substituent effects is shown in Figure
2b. Also shown is a plot for the solvolysis of tert-cumyl chloride
derivatives 8, a well studied reaction that proceeds via a carbocation
intermediate, and a plot for the SN2 displacement reaction of benzyl
chloride derivatives 9 (Figure 2a).10-12 These plots demonstrate that
the enzymatic reaction shows similar sensitivity to carbocation
stabilizing/destabilizing substituents as the tert-cumyl chloride
system (Fenz ) -3.14 ( 0.20, Fmodel ) -4.02) and the opposite
sensitivity to the benzyl chloride substitution (F ) +0.73). This
supports the previous exclusion of the SN2 mechanism and suggests
that the observed burst rate is largely a measure of the rate constant
for pyrimidine carbocation formation. This analysis also indicates
that subsequent to carbocation formation Thz-P reacts relatively
rapidly to produce TP. The rate constant for this reaction is most
likely greater than ∼20 s-1 given that no lag in TP formation was
observed, even in the case of the methoxy-substituted HMP-PP
analogue. Furthermore, information gained from this analysis
suggests that protein isomerization does not play a significant role
in limiting the rate of the burst phase.
The crystal structure of the S130A mutant of thiamin phosphate
synthase, with a trapped intermediate in the active site, has been
previously reported.6 The C7 carbon of the pyrimidine is 2.93 Å
from the closest pyrophosphate oxygen and 2.97 Å from the thiazole
nitrogen (Figure 3). As the corresponding C-O (in substrate, HMP-
PP) and C-N (in product, TP) bond lengths are 1.44 and 1.57 Å,
respectively, the structure clearly shows that there is no bonding
between the pyrimidine and the thiazole or the pyrophosphate and
suggests that the observed intermediate is a pyrimidine carbocation
Acknowledgment. This research was supported by NIH grants
DK44083 to T.P.B. and DK67081 to S.E.E.
Supporting Information Available: Detailed experimental pro-
cedures for kinetic experiments. This material is available free of charge
via the Internet at http://pubs.acs.org.
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