Allosteric Activation Shifts the Rate-Limiting Step in a Short-Form ATP Phosphoribosyltransferase

Abstract

Short-form ATP phosphoribosyltransferase (ATPPRT) is a hetero-octameric allosteric enzyme comprising four catalytic subunits (HisG_S) and four regulatory subunits (HisZ). ATPPRT catalyzes the Mg²⁺-dependent condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate (PRPP) to generate N¹-(5-phospho-β-d-ribosyl)-ATP (PRATP) and pyrophosphate, the first reaction of histidine biosynthesis. While HisG_S is catalytically active on its own, its activity is allosterically enhanced by HisZ in the absence of histidine. In the presence of histidine, HisZ mediates allosteric inhibition of ATPPRT. Here, initial velocity patterns, isothermal titration calorimetry, and differential scanning fluorimetry establish a distinct kinetic mechanism for ATPPRT where PRPP is the first substrate to bind. AMP is an inhibitor of HisG_S, but steady-state kinetics and ³¹P NMR spectroscopy demonstrate that ADP is an alternative substrate. Replacement of Mg²⁺ by Mn²⁺ enhances catalysis by HisG_S but not by the holoenzyme, suggesting different rate-limiting steps for nonactivated and activated enzyme forms. Density functional theory calculations posit an S_N2-like transition state stabilized by two equivalents of the metal ion. Natural bond orbital charge analysis points to Mn²⁺ increasing HisG_S reaction rate via more efficient charge stabilization at the transition state. High solvent viscosity increases HisG_S’s catalytic rate, but decreases the hetero-octamer’s, indicating that chemistry and product release are rate-limiting for HisG_S and ATPPRT, respectively. This is confirmed by pre-steady-state kinetics, with a burst in product formation observed with the hetero-octamer but not with HisG_S. These results are consistent with an activation mechanism whereby HisZ binding leads to a more active conformation of HisG_S, accelerating chemistry beyond the product release rate.

Allosteric control of catalysis is a widespread strategy evolved in biosynthetic pathways.¹⁻⁴ The modulation of biochemical pathways for synthetic biology applications often requires overcoming or manipulating allosteric regulation.^5,6 Furthermore, allosteric sites provide a more selective avenue for drug design in comparison with active sites, which tend to be more conserved.^3,7,8 Accordingly, the elucidation of allosteric mechanisms in multiprotein enzymatic complexes paves the way for future therapeutic and biotechnological applications.

The allosteric enzyme adenosine 5′-triphosphate phosphoribosyltransferase (ATPPRT) (EC 2.4.2.17), responsible for the first and flux-controlling step in histidine biosynthesis,⁹ is a potential drug target in some pathogenic organisms,^8,10−12 the focus of synthetic biology endeavors to harness the histidine biosynthetic pathway for histidine production in bacteria,^6,13,14 and a model system for the study of allosteric regulation of catalysis.^3,8,15,16

ATPPRT catalyzes the Mg²⁺-dependent and reversible nucleophilic substitution of adenosine 5′-triphosphate (ATP) N1 on 5-phospho-α-d-ribosyl-1-pyrophosphate (PRPP) C1 to generate N¹-(5-phospho-β-d-ribosyl)-ATP (PRATP) and inorganic pyrophosphate (PP_i) (Scheme 1),⁹ with the chemical equilibrium highly displaced toward reactants.¹⁷ The metabolic status of the cell regulates ATPPRT activity via allosteric inhibition by histidine^9,18 and orthosteric inhibition by adenosine 5′-monophosphate (AMP).¹⁹ Intriguingly, orthosteric inhibition by adenosine 5′-diphosphate (ADP) is also reported.¹⁹

Scheme 1. ATPPRT-Catalyzed Nucleophilic Substitution Reaction.

The hisG gene encodes two forms of ATPPRT. Most histidine-synthesizing organisms possess a long-form of the protein, HisG_L,^16,20 a homohexamer with each subunit consisting of two N-terminal catalytic domains and a C-terminal allosteric domain responsible for histidine inhibition.¹¹ HisG_L ATPPRTs operate by a steady-state ordered kinetic mechanism where ATP is the first substrate to bind to, and PRATP the last product to dissociate from, the enzyme.^21,22

Archaea and some eubacteria have instead a short-form of the protein, HisG_S,^23,24 a homodimer with each subunit comprising two catalytic domains homologous to HisG_L’s, but lacking the C-terminal allosteric domain.^20,25 Thus, HisG_S is catalytically active on its own but insensitive to inhibition by histidine.^20,26 HisG_S binds HisZ, the product of the hisZ gene, a catalytically inactive paralogue of histidyl-tRNA synthetase,²³ forming the hetero-octameric ATPPRT holoenzyme, where two HisG_S dimers flank a HisZ tetramer.^24,26,27 HisZ has two distinct allosteric functions: in the absence of histidine, it activates catalysis by HisG_S, and in the presence of histidine, it binds the final product of the pathway and mediates allosteric inhibition of HisG_S.^20,24,26,28 The kinetic mechanism of HisG_S ATPPRTs has not been investigated, but recent crystal structures suggest that the order of substrate binding may be different from HisG_L’s.²⁹ Moreover, little is known about the kinetics of allosteric activation.

We recently reported several crystal structures of the psychrophilic bacterium Psychrobacter arcticus dimeric HisG_S (PaHisG_S) and hetero-octameric ATPPRT holoenzyme (PaATPPRT),^26,29 from which an activation mechanism was inferred that involves tightening of the PaHisG_S dimer in the hetero-octamer when both substrates are bound (Figure 1), which facilitates leaving group stabilization at the transition state.²⁹ Here we employ initial rate studies, isothermal titration calorimetry (ITC), differential scanning fluorimetry (DSF), ³¹P nuclear magnetic resonance (³¹P NMR), liquid chromatography–mass spectrometry (LC-MS), density functional theory, solvent viscosity effects, and pre-steady-state kinetics to unveil a distinct kinetic mechanism for PaATPPRT, the role of ADP as a substrate instead of an inhibitor, the basis for charge-stabilization at the transition state, and a shift in the rate-liming step upon allosteric activation of the enzyme.

Figure 1.

PaHisG_S and PaATPPRT quaternary structures and allosteric activation. (A) PaATPPRT hetero-octamer, where catalysis is enhanced. The second PaHisG_S homodimer is behind the PaHisZ tetramer. (B) Nonactivated PaHisG_S homodimer and (C) overlay of activated and nonactivated PaHisG_S dimers. In all structures, PaHisG_S is bound to PRPP, ATP, and Mg²⁺.²⁹

Materials and Methods

Materials

ATP, PRPP, PP_i, AMP, ADP, MgCl₂, MnCl₂, D₂O (99.9 atom % deuterium), tricine, dithiothreitol (DTT), and glycerol were purchased from Sigma-Aldrich. All other chemicals were purchased from readily available commercial sources, and all chemicals were used without further purification. PaHisG_S, PaHisZ, Mycobacterium tuberculosis pyrophosphatase (MtPPase), and tobacco etch virus protease were obtained as previously published.²⁶ PRATP was produced as previously described.²⁹

PaHisG_S and PaATPPRT Activity Assay

All assays were performed under initial rate conditions in the forward direction at 20 °C as previously described²⁶ by monitoring the increase in absorbance at 290 nm due to formation of PRATP (ε_290 nm = 3600 M^–1 cm^–1)³⁰ in 1 cm path length quartz cuvettes (Hellma) in a Shimadzu UV-2600 spectrophotometer. Unless stated otherwise, for PaHisG_S activity, PaHisG_S concentration was 2.2 μM, and for PaATPPRT activity, PaHisG_S and PaHisZ concentrations were 0.38 and 15 μM, respectively. Reactions were started by addition of PRPP. Control reactions lacked either ATP, PRPP, PaHisG_S, or PaHisZ. In all kinetic experiments under the various different conditions described below, controls were carried out to ensure that the rate did not depend on MtPPase. Kinetic measurements were performed at least in duplicates unless stated otherwise.

PaATPPRT Equilibrium Dissociation Constant (K_D) in Glycerol

Initial velocities were measured in the presence of 5.6 mM ATP, 2 mM PRPP, 0.38 μM PaHisG_S, and varying concentrations of PaHisZ (0.9–8.5 μM) in 0%, (0.5–16.3 μM) in 18% and 27% glycerol (v/v). PaHisZ-PaHisG_SK_D values were obtained by fitting initial rate data to a kinetic equation (vide infra) as previously reported.²⁶

PaATPPRT and PaHisG_S Saturation Kinetics with ATP and PRPP

PaATPPRT initial rates were measured at saturating concentrations of one substrate and varying concentrations of the other, either ATP (0.4–5.6 mM) or PRPP (0.1–2.0 mM). Initial rates for PaHisG_S were determined at saturating concentrations of one substrate and varying concentrations of the other, either ATP (either 0.4–2.8 or 0.4–5.6 mM) or PRPP (0.1–2.0 mM).

PaATPPRT and PaHisG_S Saturation Kinetics with MnCl₂

PaATPPRT initial rates were measured at saturating concentrations of one substrate and varying concentrations of the other, either ATP (0.1–1.4 mM) or PRPP (0.1–2.0 mM), while initial rates for PaHisG_S (1.1 μM) were determined at saturating concentrations of one substrate and varying concentrations of the other, either ATP (0.1–1.4 mM) or PRPP (0.05–2.0 mM), in the presence of 15 mM MnCl₂ instead of MgCl₂.

Analysis of PaHisG_S Reaction with MnCl₂ by LC-MS

Reaction mixtures (500 μL) contained 100 mM tricine pH 8.5, 100 mM KCl, 4 mM DTT, 15 mM MnCl₂, 19.7 μM MtPPase, 1.4 mM ATP, 2.0 mM PRPP, and 10.3 μM PaHisG_S. Reactions were incubated for 1 h at 20 °C, after which proteins were removed by passage through 10000 MWCO Vivaspin centrifugal concentrators. Reactions were run in duplicate, and control reactions lacked PaHisG_S. LC-MS analysis of the protein-free reaction mixtures was performed on an EC250/4.6 Nucleodur 100–10 C18 ec HPLC column (10 μm × 4.6 mm × 250 mm) (Macherey-Nagel) in a 1260 infinity HPLC system coupled to a G6130B Single Quadrupole mass spectrometer (Agilent Technologies). Separation of PRATP and ATP was carried out in (A) 50 mM triethylamine-acetic acid pH 7.4 and (B) methanol as a mobile phase in the following sequence: 0–3 min 100% A, 3–3.1 min 90% A and 10% B, 3.1–12 min 80% A and 20% B at a flow rate of 1 mL min^–1, with UV absorbance monitored at 260 and 290 nm. Electrospray ionization-mass spectrometry (ESI-MS) data were acquired in negative mode with a capillary voltage of 4500 V.

PaATPPRT and PaHisG_S Saturation Kinetics in Glycerol

PaATPPRT and PaHisG_S initial rates were measured at saturating concentrations of one substrate and varying concentrations of the other, either ATP (0.4–5.6 mM) or PRPP (0.1–2.0 mM), in the presence of 0%, 18%, and 27% glycerol (v/v).

PaHisG_S Inhibition by AMP

The half-maximal inhibitory concentration of AMP was determined by measuring initial rates for PaHisG_S (4.5 μM) in the presence of 5.6 mM ATP, 2 mM PRPP, and varying concentrations of AMP (0–0.8 mM). The inhibition mechanism was investigated by measuring initial rates for PaHisG_S (4.5 μM) at saturating concentrations of one substrate and varying concentrations of the other, either ATP (0.4–5.6 mM) with different concentrations of AMP (0–0.1 mM) or PRPP (0.1–2.0 mM) with different concentrations of AMP (0–0.05 mM). PaHisG_S concentration was more than 4-fold higher than the lowest AMP concentration used, and pseudo-first-order approximation was assumed.

PaHisG_S Saturation Kinetics with ADP and PRPP

Initial rates for PaHisG_S were determined at saturating concentrations of one substrate and varying concentrations of the other, either ADP (0.4–5.6 mM) or PRPP (0.1–2.0 mM).

Comparison of PaHisG_S Reactions with ADP and ATP by ³¹P NMR Spectroscopy

Analysis of PaHisG_S reactions by ³¹P NMR spectroscopy was carried out as previously described,²⁶ except that PaHisG_S concentration was 10.3 μM and ADP replaced ATP in half of the reactions. All reactions were run in duplicate, and control reactions lacked PaHisG_S.

PaATPPRT and PaHisG_S Initial Velocity Patterns

Initial rates for PaATPPRT were measured in the presence of varying ATP (0.4–5.6 mM) and PRPP (0.1–2.0 mM), with 1 μM PaHisG_S and 20 μM PaHisZ. Initial rates for PaHisG_S were determined in the presence of varying ATP (0.2–2.8 mM) and PRPP (0.1–2.0 mM). Measurements were performed in quadruplicates.

PaHisG_S Binding by ITC

ITC measurements were carried out at 20 °C in a MicroCal PEAQ-ITC calorimeter (Malvern Instruments). Protein and ligand were solubilized in the same ATPPRT assay buffer. After a small injection of 0.4 μL, 18 successive injections of 2 μL of ligand (either 0.8 mM PRPP or 10 mM ATP) were made into 300 μL of 50 μM PaHisG_S, with 150-s intervals between successive injections and a reference power of 10 μcal s^–1. Heat of dilution for each experiment was measured by titrating ligand into assay buffer, and subtracted from the corresponding binding curve. All measurements were performed in duplicate. Data for PRPP binding were fitted to a single-site binding model as implemented in the PEAQ-ITC analysis software (Malvern Instruments).

PaHisG_S Thermal Denaturation by DSF

DSF measurements (λ_ex = 490 nm, λ_em 610 nm) were performed in 96-well plates on a Stratagene Mx3005p instrument. Thermal denaturation assays (50 μL) for 7.5 μM PaHisG_S were measured in the presence and absence of ligands (6 mM ATP, 2 mM PRPP, 208 μM PRATP, 3.6 mM PP_i), with or without 22% glycerol (v/v) (apoenzyme) in 100 mM tricine, 100 mM KCl, 4 mM DTT and 15 mM MgCl₂ pH 8.5. The assay for apoenzyme was also performed in 10 mM KH₂PO₄, 10 mM KF pH 8.0. Sypro Orange (5×) (Invitrogen) was added to all wells. Thermal denaturation curves were recorded over a temperature range from 25–93 °C with 1 °C min^–1 increments. Control curves lacked enzyme and were subtracted from curves containing enzyme. All measurements were carried out in triplicate.

Density Functional Theory Calculations

Theoretical structures were derived from B3LYP calculations using a 6-31G* basis set with a Lanl2DZ basis set on Mg²⁺ and Mn²⁺ and a Lanl2DZ pseudopotential added to Mg²⁺ and Mn²⁺ as implemented in Gaussian 09.³¹ A model system was chosen by including all residues within 5 Å of ADP and PRPP in the crystallographic dimer of the PaHisG_S-PRPP-Mg-ADP complex crystal structure²⁹ and by flipping the adenine ring from its crystal structure orientation to bring N1 in proximity to PRPP. The system was further paired down to include only functional groups, metal ions and water molecules within the 5-Å cutoff that were essential for stabilization of the transition structure. In addition to the divalent metal found in the crystal structure, a second divalent metal had to be included in the system for a transition structure to be located. Initial searches exploring structures with fixed distances along the reaction coordinate were located by performing an optimization of an input structure with the key bond-forming or bond-breaking distances held constant, and frequency calculations resulted in only one imaginary frequency along the reaction coordinate. Final transition structures for the system complexed with either Mg²⁺ or Mn²⁺ were located as stationary points with no geometrical constrains and exhibit only one imaginary frequency along the reaction coordinate. Coordinates for all optimized structures are available in the Supporting Information.

Pre-Steady-State Kinetics

Approach to steady-state in PaHisG_S and PaATPPRT reactions was investigated under multiple-turnover conditions by monitoring the increase in absorbance at 290 nm upon PRATP formation at 20 °C in an Applied Photophysics SX-20 stopped-flow spectrophotometer outfitted with a 5 μL mixing cell (0.5 cm path length and 0.9 ms dead-time). Each syringe contained 100 mM tricine pH 8.5, 100 mM KCl, 4 mM DTT, 15 mM MgCl₂, and 20 μM MtPPase. In addition, one syringe carried 40 μM PaHisG_S (with or without 100 μM PaHisZ) and 4 mM PRPP, while the other carried 11.2 mM ATP. Reaction was triggered by rapidly mixing 55 μL from each syringe. Absorbance increase with PaHisG_S was monitored in a linear-time base for 5 s with 5000 data points collected, and with PaATPPRT, in a split-time base for 2 s, with 4000 data points collected in the first 0.2 s and 4000 in the following 1.8 s. At least 8 traces were acquired for each enzyme, and controls lacked PRPP.

Data Analysis of Kinetics and Thermal Denaturation

Kinetic and DSF data were analyzed by the nonlinear regression function of SigmaPlot 13 (SPSS Inc.). Data points and error bars in graphs are represented as mean ± standard error, and kinetic and equilibrium constants are presented as mean ± fitting error. Initial rate data with varying concentrations of PaHisZ were fitted to eq 1. The concentration of PaATPPRT at any concentration of PaHisG_S and PaHisZ was calculated according to eq 2. Substrate saturation data were fitted to eq 3. Inhibition data at fixed substrate concentrations were fitted to eq 4, and competitive inhibition data were fitted to eq 5. Initial velocity patterns were fitted to eq 6, and pre-steady-state kinetics under multiple-turnover conditions was fitted to eq 7. In eqs 1–7, v is the initial rate, V_max is the maximal velocity, G is the concentration of PaHisG_S, Z is the concentration of PaHisZ, K_D is the equilibrium dissociation constant, PaATPPRT is the concentration of PaHisG_S-PaHisZ complex, S is the concentration of the varying substrate, k_cat is the steady-state turnover number, K_M is the apparent Michaelis constant, E_T is total enzyme concentration, v_i is the initial rate in the presence of inhibitor, IC₅₀ is the half-maximal inhibitory concentration, K_i is the inhibitor dissociation constant, A and B are the first and second substrates to bind to the enzyme, respectively, K_a and K_b are their respective Michaelis constants, K_ia is the apparent dissociation constant for the complex between enzyme and substrate A when the concentration of B approaches zero, t is time, P(t) is product concentration at time t, A₀ is the amplitude of the burst phase, and k_burst is the first-order rate constant of product formation in the burst phase. DSF thermal denaturation data were fitted to eq 8,³² where F_U is fraction unfolded, T is the temperature in °C, T_m is the melting temperature, c is the slope of the transition region, and LL and UL are folded and unfolded baselines, respectively.

1

2

3

4

5

6

7

8

Results and Discussion

PaHisG_S and PaATPPRT Kinetic Mechanism

A steady-state ordered kinetic mechanism in which ATP is the first substrate to bind to the enzyme, and PRATP is the last product to dissociate from it, has long been demonstrated for HisG_L ATPPRTs.^21,22 This mechanism has been supported by several structures of Campylobacter jejuni and M. tuberculosis ATPPRT-ATP binary complexes,^10,16 and by the recent structure of the C. jejuni ATPPRT catalytic core in complex with PRPP, where despite being able to bind to the free enzyme, PRPP drifts into the ATP binding site, which would lead to a dead-end complex.³³ The kinetic mechanism of HisG_S ATPPRTs, on the other hand, has not been explored. We recently published the crystal structures of PaHisG_S and PaATPPRT in binary complexes with PRPP and PRATP, and in ternary complexes with PRPP-ATP, but were unable to obtain structures of enzyme-ATP binary complexes, suggesting a reverse order of substrate binding in comparison with HisG_L ATPPRTs.²⁹

To test this hypothesis, the kinetic mechanism of PaHisG_S and PaATPPRT was investigated. Intersecting patterns of double-reciprocal plots with both ATP and PRPP in initial velocity studies were determined for PaATPPRT (Figure 2A,B) and PaHisG_S (Figure 2C,D), indicating a ternary complex is formed in a sequential mechanism. The double-reciprocal plots intersecting to the left of the y-axes rule out a rapid equilibrium ordered mechanism.³⁴ Fitting the data to eq 6 (Figure 2E,F) yielded steady-state kinetic parameters summarized in Table S1.

Figure 2.

Initial velocity patterns for PaATPPRT and PaHisG_S. Intersecting double-reciprocal plots for PaATPPRT with (A) ATP and (B) PRPP as varying substrates and for PaHisG_S with (C) ATP and (D) PRPP as varying substrates. Each color represents a different fixed concentration of the cosubstrate. Data points are mean ± SE. Three-dimensional plot of (E) PaATPPRT and (F) PaHisG_S initial rate data, where lines are data fitting to eq 6.

Binding studies were performed with PaHisG_S to elucidate the substrate binding order. Binding of PRPP to PaHisG_S was detected by ITC (Figure S1), and fitting the data from two independent experiments to a single-site binding model (stoichiometry of 1:1 and no cooperativity) resulted in K_D's of 15.4 ± 0.2 and 8.3 ± 0.1 μM (one from each experiment, yielding a mean ± SE of 12 ± 2 μM). ATP binding to PaHisG_S, on the other hand, could not be detected, as no signal was observed beyond heat of dilution (Figure S2). This corroborates the hypothesis that PRPP can bind to the free enzyme, while ATP cannot.

To confirm and expand these results, PaHisG_S thermal denaturation curves in the presence and absence of substrates and products were determined by DSF (Figure 3), and data fitting to eq 8 produced T_m’s shown in Table S2. PRPP and PRATP increased PaHisG_ST_m by 6 and 5 °C, respectively, indicating that these molecules can bind to the free enzyme. Conversely, ATP and PP_i did not alter PaHisG_ST_m. The latter observation alone does not necessarily rule out the possibility that ATP and PP_i can bind to the free enzyme, but the integration of crystallography,²⁹ initial velocity patterns, ITC, and DSF data supports a steady-state ordered mechanism where PRPP is the first substrate to bind to PaHisG_S and PRATP is the last product to dissociate from it. The strong parallels in corresponding binding modes seen in the PaHisG_S and PaATPPRT crystal structures²⁹ suggest that PaATPPRT follows the same mechanism. Moreover, given the conservation of PRPP position in PaATPPRT²⁹ and Lactococcus lactis ATPPRT binary complexes,²⁷ this mechanism may be valid for other HisG_S ATPPRTs.

Figure 3.

DSF-based thermal denaturation of PaHisG_S apoenzyme and in the presence of substrates and products. Thin black lines are data fitting to eq 8.

AMP Is an Inhibitor of PaHisG_S

AMP is a competitive inhibitor of HisG_L ATPPRTs against both substrates,^16,19 which is explained structurally by the simultaneous partial occupation of the PRPP and ATP binding sites by AMP’s phosphoribosyl and adenine moieties, respectively.^11,16,35 AMP is also a competitive inhibitor against PRPP in L. lactis ATPPRT,²⁸ and the recent crystal structure of the PaHisG_S-AMP complex shows a similar binding mode as in HisG_L ATPPRTs.^11,16,29,35 AMP inhibits PaHisG_S with an IC₅₀ of 79 ± 6 μM (Figure S3A), and inhibition is competitive against both PRPP and ATP, with K_i’s of 25 ± 5 and 52 ± 8 μM, respectively (Figure S3B,C). These values are on average ca. 7- and 10-fold lower than those for HisG_L ATPPRTs,^16,19 and over 27-fold lower than that for L. lactis ATPPRT,²⁸ suggesting PaHisG_S activity is more stringently regulated by this metabolite.

ADP Is a Substrate for PaHisG_S

ADP has been shown to be an inhibitor of HisG_L ATPPRTs.¹⁹ However, crystal structures of PaHisG_S and PaATPPRT in complex with PRPP-ADP reveal that ADP binds in the same manner as ATP.²⁹ In order to evaluate the ability of PaHisG_S to use ADP as a substrate, we compared the reactions with ADP and ATP by ³¹P NMR spectroscopy (Figure S4). The spectra of reactions containing ADP (Figure S4A) and ATP (Figure S4C) are similar except for the peak at −19.2 to −19.4 corresponding to the γ-PO₄^2– phosphorus of ATP and PRATP, since this group is absent in ADP and N¹-(5-phospho-β-d-ribosyl)-ADP (PRADP). Spectra for both reactions differ from the controls lacking PaHisG_S (Figure S4B,D). The characteristic peak at ca. 3.3 ppm corresponding to the phosphorus in the N¹-5-phospho-β-d-ribose moiety of the product²⁶ is present in the reaction spectra with ADP (Figure S4A, inset) and ATP (Figure S4C, inset), and absent in the controls (Figure S4B,D, insets), establishing that ADP can replace ATP as a substrate for PaHisG_S.

For a quantitative comparison of the reactions with ATP and ADP, steady-state kinetic analysis of the reaction with either substrate was carried out (Figure 4) and kinetic parameters are summarized in Table S3. Values of k_cat are the same within error with either ATP or ADP as a substrate, indicating that once saturated PaHisG_S turns over ATP and ADP just as effectively. The main difference is in the K_M for ADP, which is over 3-fold that for ATP, suggesting some small loss of affinity for the steady-state with ADP.

Figure 4.

PaHisG_S substrate saturation curves with either ATP (green) or ADP (blue) as a substrate. (A) Varying PRPP concentration with saturating concentration of the nucleotide. (B) Varying the nucleotide concentration with saturating concentration of PRPP. Data points are mean ± SE, and lines are data fitting to eq 3.

PaHisG_S and PaATPPRT Kinetics with Mn²⁺

Replacement of Mg²⁺ by Mn²⁺ is a common strategy in enzymology,³⁶ having been employed to uncover rate-limiting steps in reactions involving stabilization of phosphate groups.³⁷ HisG_L ATPPRTs have been reported to have their activities either unaltered or decreased by changing the divalent metal in the reaction from the physiological Mg²⁺ to Mn²⁺, but no mechanistic inference has been drawn.^17,38 To evaluate the effect of Mn²⁺ on a HisG_S enzyme, saturation curves for PaHisG_S and PaATPPRT with either divalent metal were determined (Figure 5), and kinetic constants are displayed in Table S4. Mn²⁺ led to 2.6- and 11-fold increases in PaHisG_Sk_cat and k_cat/K_M^ATP, respectively, as compared with Mg²⁺. The change in k_cat/K_M^ATP was driven in large part by a reduction in K_M^ATP. LC-MS analysis of the PaHisG_S reaction with Mn²⁺ confirmed the same product, PRATP, was being formed (Figure S5).

Figure 5.

Steady-state kinetics with Mg²⁺ (green) and Mn²⁺ (blue). Saturation curves varying either PRPP or ATP concentration with saturating concentration of the cosubstrate for (A and B) PaHisG_S and (C and D) PaATPPRT. Data points are mean ± SE, and lines are data fitting to eq 3.

In contrast to PaHisG_S, steady-state constants for PaATPPRT were unchanged by Mn²⁺, except for a 2.9-fold increase in k_cat/K_M^ATP owing to a reduction in K_M^ATP. These results raise the possibility that PaHisG_S and PaATPPRT reactions have distinct rate-limiting steps. Crystal structures of PaHisG_S and PaATPPRT with various ligands do not depict any specific interaction between Mg²⁺ and the enzyme,²⁹ raising the possibility the off-rates of products from the active site might not be affected by the nature of the metal ion. It is possible, nonetheless, that a solution metal stabilizes charges of either PRATP or PP_i concomitantly with product release from the enzyme. The metal ion seen in the structures acts as a Lewis acid to stabilize negative charges in the Michaelis complex upon binding of ATP, with a putative second metal ion likely present at the transition state to facilitate departure of the PP_i leaving group.²⁹ Thus, one might expect Mn²⁺ to increase the reaction rate if rate-limiting steps are located between ATP binding to the enzyme-PRPP complex and product formation, since a stronger Lewis acid would facilitate catalysis by stabilizing charges more efficiently. The kinetic constants affected would be k_cat and k_cat/K_M^ATP, which is exactly what is observed with PaHisG_S. If, on the other hand, ternary complex formation played a minor role in limiting the reaction rate, chemistry was fast, and product release was the slowest step, a modest increase in k_cat/K_M^ATP only would be expected, which is the case with PaATPPRT.

A Transition-State Hypothesis for the PaHisG_S Reaction

An S_N1-like, D_N*A_N^‡39,40 transition-state structure has recently been proposed for C. jejuni and M. tuberculosis (HisG_L) and L. lactis (HisG_S) ATPPRT-catalyzed reaction based on kinetic isotope effects and computational chemistry, using a simplified model of the reaction for density functional theory calculations.¹⁰ Having established that PaHisG_S utilizes ADP as a substrate with a similar k_cat as it does ATP (Table S3), the crystal structure of the PaHisG_S-PRPP-Mg-ADP Michaelis complex²⁹ served as a starting point for density functional theory calculations in order to find a theoretical transition state for the reaction that includes not only the full substrates but also several active-site residue side-chain surrogates and water molecules essential to stabilize the system, with either Mg²⁺ or Mn²⁺ as the metal ion (Figure 6). Transition structures were located as stationary points (i.e., without any constraints on distances or dihedral angles) and possess only one imaginary frequency reflecting vibration along the N1–C1–O1 axis. Inclusion of a second equivalent of the divalent metal ion to stabilize the departing PP_i leaving group was essential to locate transition structures, lending support to a recent proposal based on the crystal structures of PaHisG_S and PaATPPRT Michaelis complexes²⁹ and the transition structures of other phosphoribosyltransferases.⁴¹

Figure 6.

Transition-state model for the PaHisG_S-catalyzed reaction. (A) Transition structure with magnesium, (B) transition structure with manganese, and (C) overlay of the transition structures with magnesium and manganese. Substrates are represented as stick models, side-chain mimics as wireframe, and metal ions and water oxygens as spheres. Carbon is in either cyan or yellow for substrates and in gray for side-chain mimics, with oxygen in red, nitrogen in blue, phosphorus in orange, magnesium in green, and manganese in purple. Hydrogens are omitted for simplicity. Partial bonds and metal ion coordination bonds are represented by dashed lines. Distances are shown for the N1–C1 and the C1–O1 bonds. Key residue side-chain mimics are labeled, and the prime denotes a residue of the adjacent subunit in the PaHisG_S dimer.²⁹

The optimized structures indicate an S_N2-like, almost synchronous A_ND_N transition state is possible for the PaHisG_S-catalyzed reaction with either Mg²⁺ (Figure 6A) or Mn²⁺ (Figure 6B) as a Lewis acid. The 6-NH₂ group of ADP is protonated in all transition structures and is likely to lose a proton to form the 6-NH group of PRADP only after the nucleophilic substitution is complete, as recently hypothesized.²⁹ Nucleophilic attack occurs from the charge-neutral resonance structure of adenine in which N1 has transiently a negative charge due to electron donation from N6. This natural resonance structure represents 6.64% of the distribution of adenine resonances.⁴² The A_ND_N transition state located here contrasts with the D_N*A_N^‡ one proposed for HisG_L and HisG_S ATPPRT reaction.¹⁰ This would mean that different orthologues of ATPPRT catalyze the same reaction via different transition states, which is not uncommon in ribosyl-transfer reactions. For instance, distinct transition-state models based on kinetic isotope effects and density functional theory have been suggested for bovine and human purine nucleoside phosphorylases,^43,44 and for wild-type and mutant human purine nucleoside phosphorylases.^43,45 Kinetic isotope effect measurements for PaHisG_S could test the A_ND_N transition-state hypothesis put forth in this work.

Overlay of the transition structures with Mg²⁺ and Mn²⁺ demonstrates an almost identical arrangement (Figure 6C), indicating transition-state geometry cannot explain the discrimination in PaHisG_S reactivity between the metal ions. Natural bond orbital (NBO) analysis of the transition structures, however, revealed significant differences in charge distribution in the metal ions and the PP_i at the transition state depending on which metal is included (Table S5). Most atoms have very similar charges in the two transition structures, except for the metal ions and PP_i oxygens. The average charge of the two magnesium ions at the transition state is 1.439, over 2-fold higher than the average charge of the manganese ions, 0.649. This is due to more efficient attenuation of the negative charge of the PP_i leaving group by Mn²⁺ through d-orbital bonding to coordinating oxygens, as shown by orbital population analysis. As compared with Mg²⁺, therefore, Mn²⁺ improves catalysis in the PaHisG_S reaction by more effectively stabilizing the negatively charged leaving group at the transition state.

Solvent Viscosity Effects on PaHisG_S and PaATPPRT Kinetics

In order to probe further the distinct rate-limiting steps governing PaHisG_S and PaATPPRT catalyses, the effect of solvent viscosity on reaction rates was evaluated (Figure 7), and the data are summarized in Tables S6 and S7. Increasing solvent viscosity by increasing glycerol concentration⁴⁶ slows down diffusional steps such as substrate binding and release and product release, and values of kinetic constants will be reduced if such steps are rate-limiting.⁴⁷⁻⁴⁹PaHisG_S rate constants did not decrease with increasing glycerol concentration (Table S6), consistent with diffusional steps not contributing to limit the reaction rate. Instead, as shown in Figure 7A and Table S6, glycerol led to an increase in PaHisG_Sk_cat and k_cat/K_M^PRPP of up to 2.7- and 2.4-fold, respectively, while k_cat/K_M^ATP was only marginally affected. Inverse solvent viscosity effects generally suggest that a more active dynamic conformation of the enzyme or the Michaelis complex is favored at high viscosity.⁴⁷⁻⁴⁹ To rule out the possibility that glycerol might be affecting the overall stability of the enzyme, a thermal denaturation curve was determined by DSF in 22% glycerol (Figure S6), and no difference in T_m was observed in comparison with that determined without glycerol (Table S2). Crystal structures of PaHisG_S apoenzyme and PaHisG_S-PRPP-ATP were also obtained with and without soaking crystals in glycerol, and no electron density for glycerol was visualized in any of the structures.²⁹ This suggests that glycerol is acting as part of bulk solvent, not as a ligand, but with the caveat that crystal lattice might have prevented binding.

Figure 7.

Solvent viscosity effects on steady-state kinetics determined at 0% (green), 18% (pink), and 27% (cyan) glycerol (v/v). (A) PaHisG_S saturation curves (top) and steady-state constants (bottom) dependence on glycerol concentration. (B) PaATPPRT saturation curves (top) and steady-state constants (bottom) dependence on glycerol concentration. Data represent either mean ± SE (scatter plots) or value ± fitting error (bar plots). Lines are data fitting to eq 3.

To assess the effect of solvent viscosity on PaATPPRT, first the K_D for the PaHisG_S-PaHisZ complex had to be measured in glycerol (Figure S7), and data fitting to eq 1 yielded K_D’s of 1.3 ± 0.1, 1.1 ± 0.2, and 0.5 ± 0.1 μM in 0%, 18%, and 27% glycerol, respectively. Knowledge of the K_D’s allowed calculation, using eq 2, of PaATPPRT concentrations at different glycerol concentrations for measurement of k_cat. In contrast to the effect on PaHisG_S, increasing solvent viscosity resulted in a decrease of up to 2.5-fold in PaATPPRT k_cat, with negligible effects on k_cat/K_M for either substrate, as shown in Figure 7B and Table S7. This points to product dissociation from PaATPPRT as the rate-limiting step in the reaction, as is the case with HisG_L ATPPRTs.^8,50

Burst in Product Formation by PaATPPRT

To glean additional support for distinct rate-limiting steps controlling nonactivated and activated PaHisG_S reactions, product formation time courses were monitored under pre-steady-state conditions for PaHisG_S and PaATPPRT (Figure 8). PRATP formation with PaHisG_S varies linearly with time with a steady-state rate constant of 0.091 ± 0.001 s^–1, in reasonable agreement with k_cat (Tables S3, S4, S6). This rules out a slow step after formation of enzyme-bound products⁵¹ and suggests interconversion between ternary complexes (k₅ + k₆ in Scheme 2) is rate-limiting.

Figure 8.

Pre-steady-state kinetics with PaATPPRT and PaHisG_S, with a burst in product formation observed with the former but not the latter. Black lines are data fitting to eq 7 for PaATPPRT and a linear regression for PaHisG_S.

Scheme 2. Interpretation of the Pre-Steady-State of PaHisG_S and PaATPPRT Reactions.

On the other hand, a burst in PRATP formation precedes the steady-state with PaATPPRT, and data fitting to eq 7 yielded a k_burst of 80 ± 1 s^–1, a steady-state rate constant of 1.11 ± 0.01 s^–1, and an A₀ of 4.3 μM. This is consistent with a step after chemistry, likely product release (k′₇ in Scheme 2), limiting the reaction rate,^51,52 in agreement with the conclusion drawn from solvent viscosity effects. M. tuberculosis HisG_L ATPPRT also displays a burst in product formation with a k_burst of 0.67 s^–1 at 25 °C.⁸ Thus, PaATPPRT k_burst at 20 °C is over 119-fold higher than M. tuberculosis HisG_L ATPPRT’s at 25 °C, which may be a feature of HisG_S ATPPRTs and/or a consequence of PaATPPRT being psychrophilic.²⁶

The amplitude of the burst phase (A₀) generally reflects the concentration of the Michaelis complex, which at saturating substrate concentrations could be as high as the concentration of enzyme.⁵³ The A₀ of 4.3 μM is over 4.4-fold lower than the concentration of PaATPPRT used in the experiment (19 μM). Two main reasons may account, separately or in combination, for this result without invoking the unlikely scenario where ca. 75% of enzyme molecules are inactive. First, the enzyme might not be fully saturated by one or both substrates, which would also explain the steady-state rate constant being slightly smaller than the k_cat values extrapolated from substrate saturation curves. This may be the case with the PaHisG_S steady-state rate constant as well. Second, chemical reversibility decreases A₀. Both k_burst and A₀ are dependent on all rate constants depicted in Scheme 2, the forward and reverse rate constants for interconversion between enzyme-bound substrates and products, k₅ and k₆, respectively, and the net rate constant for release of products from the enzyme, k′₇, according to eqs 9 and 10.⁵¹

9

10

Upon inspection of eqs 9 and 10, one must conclude that under the most favorable conditions, full expression of A₀ can only occur when chemistry is irreversible (k₆ = 0) and much faster than product release (k₅ ≫ k′₇). Internal reversibility, described by the magnitude of k₆, will increase k_burst while decreasing A₀. Equilibrium in the ATPPRT reaction strongly favors the reactants,¹⁷ making it possible for the crystal structure of the PaATPPRT-PRPP-ATP ternary-complex to be attained with wild-type enzyme.²⁹ Hence, k₆ is likely to be much larger than k₅, making k₆ the main contributor to k_burst and significantly reducing A₀ from its theoretical upper limit of 19 μM. Relative contributions of k₅ and k₆ to k_burst and A₀ notwithstanding, it is clear that activation of PaHisG_S by PaHisZ switches the rate-limiting step of the reaction from interconversion between the ternary complexes to product release.

PaHisZ-Induced Shift in the Rate-Limiting Step

The results presented here demonstrate that two long-established mechanistic features of HisG_L ATPPRTs, namely, ATP as the first substrate to bind to the enzyme and ADP as an inhibitor,^{16,19,21,22,33} do not apply to PaHisG_S, and possibly other HisG_S ATPPRTs. Providing functional data to support hypotheses proposed based on extensive crystallography work on PaHisG_S and PaATPPRT,²⁹PaHisG_S is shown to be able to replace ATP for ADP as a substrate and to operate by a steady-state ordered mechanism where PRPP is the first substrate to bind to the enzyme (Scheme 3). PaHisG_Sk_cat increases when Mn²⁺ replaces Mg²⁺, which can be accounted for owing to more efficient charge stabilization by Mn²⁺ upon leaving group departure at the transition state. The observation that PaATPPRT steady-state kinetics is unaltered with Mn²⁺ raises the possibility of k_cat’s for the activated and nonactivated enzyme forms reporting on distinct steps. This is confirmed by solvent viscosity effects on steady-state parameters and by pre-steady-state kinetics under multiple-turnover conditions, which indicate that interconversion between PaHisG_S–PRPP-ATP and PaHisG_S–PRATP-PP_i complexes limits the reaction rate for the nonactivated enzyme, likely with a significant contribution from chemistry given the effect of Mn²⁺. However, allosteric activation by PaHisZ accelerates this interconversion well beyond the steady-state rate, which now reflects the off-rate of either PP_i from the PaATPPRT–PRATP-PP_i ternary complex or PRATP from the PaATPPRT–PRATP binary complex (Scheme 3). This provides fundamental insight into the allosteric regulation of a complex multiprotein enzyme.

Scheme 3. Kinetic Mechanism and Rate-Limiting Steps of PaHisG_S (top) and PaATPPRT (bottom) Reactions and the Corresponding Crystal Structures^26,29 .

The second PaHisG_S homodimers lie behind the PaHisZ tetramers.

Glossary

Abbreviations

ATP

adenosine 5′-triphosphate

AMP

adenosine 5′-monophosphate

ADP

adenosine 5′-diphosphate

ATPPRT

ATP phosphoribosyltransferase

PRPP

5-phospho-α-d-ribosyl-1-pyrophosphate

PRATP

N¹-(5-phospho-β-d-ribosyl)-ATP

PP_i

inorganic pyrophosphate

DTT

dithiothreitol

ITC

isothermal titration calorimetry

DSF

differential scanning fluorimetry

LC-MS

liquid chromatography–mass spectrometry

PaATPPRT

P. arcticus ATPPRT

PaHisG_S

P. arcticus HisG_S

PaHisZ

P. arcticus HisZ

³¹P NMR

³¹P nuclear magnetic resonance

MtPPase

Mycobacterium tuberculosis inorganic pyrophosphatase

MWCO

molecular weight cut off

ESI-MS

electrospray ionization mass spectrometry

K_D

equilibrium dissociation constant

EcPRPPS

E. coli PRPP synthetase

PRADP

N¹-(5-phospho-β-d-ribosyl)-ADP

Supporting Information Available

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.biochem.8b00559.

• ITC curves, PaHisG_S inhibition by AMP, spectra, DSF-based thermal denaturation of PaHisG_S, determination of equilibrium dissociation, PaATPPRT and PaHisG_S steady-state parameters from initial velocity patterns, PaHisG_ST_m’s by DSF in the presence and absence of ligands, steady-state kinetic constants, effect of Mn²⁺ on PaATPPRT and PaHisG_S steady-state kinetic parameters, NBO charge distribution, solvent viscosity effects, and coordinates for all transition structures (PDF)

The authors declare no competing financial interest.