Cryptosporidium parvum IMP Dehydrogenase - The Journal of

THE JOURNAL OF BIOLOGICAL CHEMISTRY © 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

Vol. 279, No. 39, Issue of September 24, pp. 40320 –40327, 2004 Printed in U.S.A.

Cryptosporidium parvum IMP Dehydrogenase IDENTIFICATION OF FUNCTIONAL, STRUCTURAL, AND DYNAMIC PROPERTIES THAT CAN BE EXPLOITED FOR DRUG DESIGN* Received for publication, June 24, 2004, and in revised form, July 15, 2004 Published, JBC Papers in Press, July 21, 2004, DOI 10.1074/jbc.M407121200

Nwakaso N. Umejiego‡§, Catherine Li‡, Thomas Riera¶, Lizbeth Hedstrom¶, and Boris Striepen‡储** From the ‡Department of Cellular Biology and 储Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602 and the ¶Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454

The protozoan parasite Cryptosporidium parvum causes severe enteritis with substantial morbidity and mortality among AIDS patients and young children. No fully effective treatment is available. C. parvum relies on inosine 5ⴕ-monophosphate dehydrogenase (IMPDH) to produce guanine nucleotides and is highly susceptible to IMPDH inhibition. Furthermore, C. parvum obtained its IMPDH gene by lateral transfer from an epsilon-proteobacterium, suggesting that the parasite enzyme might have very different characteristics than the human counterpart. Here we describe the expression of recombinant C. parvum IMPDH in an Escherichia coli strain lacking the bacterial homolog. Expression of the parasite gene restores growth of this mutant on minimal medium, confirming that the protein has IMPDH activity. The recombinant protein was purified to homogeneity and used to probe the enzyme’s mechanism, structure, and inhibition profile in a series of kinetic experiments. The mechanism of the C. parvum enzyme involves the random addition of substrates and ordered release of products with rate-limiting hydrolysis of a covalent enzyme intermediate. The pronounced resistance of C. parvum IMPDH to mycophenolic acid inhibition is in strong agreement with its bacterial origin. The values of Km for NAD and Ki for mycophenolic acid as well as the synergistic interaction between tiazofurin and ADP differ significantly from those of the human enzymes. These data suggest that the structure and dynamic properties of the NAD binding site of C. parvum IMPDH can be exploited to develop parasitespecific inhibitors.

Cryptosporidium parvum is one of the most common causes of waterborne infectious disease in the United States. In 1993, an outbreak in Milwaukee, Wisconsin, involved an estimated 403,000 cases of symptomatic illness, resulting in a significant number of deaths (1). Cryptosporidiosis is marked by watery

* This work was partly funded by National Institutes of Health Grants AI48475 (to B. S.), AI55268 (to B. S.), and GM54403 (to L. H.) and additional support from Merck Research Laboratories (to B. S.) and Biota, Inc. (to L. H.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. § A University of Georgia Center for Undergraduate Research Opportunities and Biomedical and Health Sciences Institute summer research fellow. ** To whom correspondence should be addressed: Dept. of Cellular Biology, 724 Biological Sciences Bldg., University of Georgia, Athens, GA 30602. Tel.: 706-583-0588; Fax: 706-542-7142; E-mail: striepen@ cb.uga.edu.

diarrhea, causing pronounced dehydration, abdominal pain, and weight loss. Treatment is currently limited to fluid and electrolyte replacement to prevent dehydration (2). The symptoms of acute cryptosporidiosis can be severe but are usually limited to 1–2 weeks duration, after which patients develop protective immunity, and the disease resolves spontaneously. However, patients with weakened immune systems suffer from persistent chronic disease that often becomes life-threatening (3, 4). Effective drug treatment is urgently needed for the management of cryptosporidiosis, especially in AIDS patients. The nucleotide biosynthetic pathways provide the precursors for DNA and RNA synthesis and are a rich source of drug targets. Fast replication rates make microbes especially sensitive to drugs affecting the nucleotide pools. Recent genomic and experimental studies suggest that Cryptosporidium parvum uses a minimal set of enzymes in highly streamlined nucleotide biosynthetic pathways. Whereas most parasitic protozoa salvage purines from the host and synthesize pyrimidines de novo, C. parvum relies on salvage for both purine and pyrimidine nucleotides (5). C. parvum scavenges adenosine from the host cell via adenosine kinase to produce AMP (Fig. 1A). AMP enters the adenine nucleotide pool or is converted to GMP by the sequential action of AMP deaminase, inosine 5⬘-monophosphate dehydrogenase (IMPDH),1 and GMP synthase. C. parvum lacks the enzymes required to salvage purine bases and will therefore be highly susceptible to the inhibition of any step in this pathway. The IMPDH inhibitors ribavirin and mycophenolic acid (MPA) block C. parvum development in tissue culture (5, 6), and ribavirin is effective in the neonatal mouse model,2 which validates IMPDH as a target for treatment of cryptosporidiosis. Moreover, IMPDH is a well developed target for antiviral and immunosuppressive therapy, and several inhibitors of human IMPDH are already in clinical use (7–10), so the design of parasite-specific IMPDH inhibitors will be greatly facilitated by the ability to “piggy-back” on existing drug development programs. The IMPDH reaction is unusual in that it involves a large conformational change in midcatalytic cycle (Fig. 1D). In the rapid redox phase of the reaction, IMP and NAD bind randomly, the active site Cys attacks IMP, and hydride is trans1 The abbreviations used are: IMPDH, inosine 5⬘-monophosphate dehydrogenase; XMP, xanthosine 5⬘-monophosphate; ␤-CH2-TAD, ␤-methylene thiazole-4-carboxamide adenine dinucleotide; TAD, thiazole-4-carboxamide adenine dinucleotide; APAD, 3-acetylpyridine adenine dinucleotide; NHD, nicotinamide hypoxanthine dinucleotide; APADH, reduced 3-acetylpyridine adenine dinucleotide; NHDH, reduced nicotinamide adenine dinucleotide; MZP, mizoribine monophosphate; MPA, mycophenolic acid; MALDI-TOF, matrix-assisted laser desorption ionization time-of-flight. 2 J. R. Mead and B. Striepen, unpublished results.

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Cryptosporidium IMPDH

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FIG. 1. Purine metabolism and IMPDH reaction in C. parvum. A, purine salvage in C. parvum (parasite). Note that in comparison with the mammalian host, the parasite pathway is highly streamlined and that IMPDH is an essential enzyme (A, adenine; Ado, adenosine; G, guanine, H, hypoxanthine). B, mechanism of the IMPDH reaction and structure of substrate and products. C, structure of IMPDH inhibitors used in this study. D, two mobile elements of IMPDH undergo conformational changes during enzyme catalysis. An active site loop (loop) carrying the catalytic cysteine residue moves into the active site after IMP binding. The flap covering the IMP and parts of the NAD site (flap) has to fold into the closed conformation for the hydrolysis of the E-XMP* complex to occur.

ferred to NAD, producing E-XMP* (Fig. 1, B and D) (11). NADH is released, and a flap moves into the vacant site, changing the enzyme into a hydrolase. E-XMP* is hydrolyzed, and XMP is released. The hydrolysis of E-XMP* is at least partially ratelimiting in all IMPDH reactions studied so far (12–15). Several inhibitors compete with the flap for the vacant NADH site, thus preventing the hydrolysis of E-XMP* (Fig. 1, C and D). The selectivity of these inhibitors is determined by both the structure of the NADH binding site and the dynamic properties of the flap. For example, MPA traps the E-XMP* intermediate by binding in the nicotinamide portion of the vacant NADH site. Two residues in the nicotinamide site are not conserved; mammalian enzymes contain Arg322 and Gln441 (human type 2 numbering), which favor MPA binding, whereas microbial enzymes contain Lys and Glu at these positions (see Fig. 5). In addition, the open conformation is favored in mammalian enzymes, whereas the closed conformation of the flap is favored in microbial enzymes (14, 16). Thus, MPA is a potent inhibitor of mammalian IMPDHs but a poor inhibitor of microbial enzymes. In contrast, MZP binds in the IMP site and induces the closed conformation (16). Thus, although the residues of the IMP site are highly conserved, the dynamic properties of the flap make MZP a more potent inhibitor of microbial enzymes. We have recently isolated the gene coding for C. parvum IMPDH (17). Surprisingly, phylogenetic analyses demonstrate that this gene groups consistently with eubacteria, although C. parvum is clearly a eukaryote (17). This observation suggests that the IMPDH gene was transferred from a bacterium, a process that plays an unexpectedly important role in the evolution of the C. parvum metabolism (5, 17, 18). Prokaryotic

and eukaryotic IMPDHs show significant differences in their kinetic properties and inhibition profiles (19 –22), so the divergent phylogenetic origins of host and parasite enzymes present a promising opportunity for the development of parasite-specific inhibitors. To test this hypothesis, we expressed the gene coding for C. parvum IMPDH in Escherichia coli, purified recombinant protein to homogeneity, and subjected the enzyme to a series of kinetic experiments probing its mechanism, structure, and inhibition. These analyses reveal pronounced differences between the C. parvum and human IMPDH and suggest a strategy for the design of parasite-specific inhibitors. EXPERIMENTAL PROCEDURES

Materials—IMP, ADP, xanthosine 5⬘-monophosphate, NADH, GMP, 3-acetylpyridine adenine dinucleotide (APAD), and Trizma base were purchased from Sigma. NAD⫹ was purchased from Roche Applied Science. Dithiothreitol was purchased from Research Organics, Inc. Glycerin, EDTA, and KCl were purchased from Fisher. Molecular Methods—The coding sequence of C. parvum IMPDH was amplified by PCR, generating artificial flanking restriction sites for BamHI and HindIII using primers 5⬘-CGTAGGATCCATGGGTACAAAAAACATAGGAAAAGG-3⬘ and 5⬘-TACGAAGCTTCTATTTACTATAATTCATTACTT-3⬘ and plasmid pCpIMPDHComp as template. This plasmid was originally obtained from a complemented T. gondii clone obtained in a genetic screen using a C. parvum genomic library (17). The plasmid contained a 1387-bp insert including the entire C. parvum IMPDH coding region (17). The resulting molecule was purified, digested with BamHI and HindIII, and ligated into plasmid pTactac digested with the same enzymes (23). The resulting expression plasmid pTacCpIMPDH was characterized by restriction mapping and complete sequencing of the insert. Expression and Purification of C. parvum IMPDH—pTacCpIMPDH was transformed into E. coli strain TX685, which lacks endogenous IMPDH due to a deletion in the GuaB locus (24). To test for comple-

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FIG. 2. Expression and purification of recombinant C. parvum IMPDH. A, C. parvum IMPDH complementation of TX685 E. coli. IMPDH-deficient TX685 E. coli carrying no plasmid (TX685), pTactac plasmid alone (TX685/ptac), and pTacCpIMPDH (TX685/ptacCpIMPDH), were plated onto nonselective LB agar plates and minimal medium (MM) plates. All cells grew equally well on LB (upper panel). However, only the C. parvum IMPDH construct was able to complement the lack of guanine synthesis in TX685 cells (lower panel). B, SDS-PAGE of the purification of recombinant C. parvum IMPDH. Lane 1, molecular mass standards; masses in kDa are noted along the left of the gel; lane 2, crude extract (190 ␮g); lane 3, C. parvum IMPDH after the Cibacron blue agarose column (7 ␮g); lanes 4 – 8, C. parvum IMPDH after the IMP affinity column (6, 11, 17, 24, and 28 ␮g, respectively). C, MALDI-TOF mass spectrometry spectrum of C. parvum IMPDH. A mass of 42,904 Da is measured for the main peak (two minor peaks representing dimer [2M ⫹ H⫹] and double protonated monomer [M ⫹ 2H⫹] are also detected). D, C. parvum IMPDH was sized on a 30-cm Sepharose 6 HR gel filtration column on a BIOCAD SPRINT perfusion chromatography system. The size exclusion profile was standardized using a mixture of proteins with molecular masses as indicated at their respective elution positions (see “Experimental Procedures” for details). C. parvum IMPDH eluted as a single peak and with a size consistent with a homotetramer. mentation, bacteria were plated on LB and minimal medium agar plates containing glucose, essential salts, and amino acids but lacking guanine nucleotides. For enzyme production, cells carrying the pTacCpIMPDH plasmid were grown overnight and diluted 10-fold into 1 liter of fresh LB broth containing 100 ␮g/ml ampicillin. After shaking at 37 °C for 1 h, isopropyl-1-thio-␤-galactopyranoside was added to the culture to a concentration of 1 mM to induce overexpression of IMPDH. The cells were allowed to grow for 16 h, at which time they were harvested by centrifugation and washed twice in buffer A (50 mM Tris, pH 8, 1 mM dithiothreitol, and 10% glycerol), resuspended in 25 ml of buffer A, and frozen at ⫺20 °C. Cells were later thawed on ice, supplemented with 2.5 ml of reconstituted protease inhibitor mixture (Calbiochem), and lysed by sonication. After centrifugation at 12,000 rpm for 30 min, the cleared supernatant (IMPDH activity ⫽ 0.08 ␮mol of product/min/mg) was applied to a Sigma Cibacron blue agarose column previously equilibrated with buffer A at 4 °C (21). IMPDH was eluted in a linear gradient of 0 –2 M KCl in buffer A. Fractions containing IMPDH activity were pooled (IMPDH activity ⫽ 0.41 ␮mol of product/min/mg) and applied to an IMP affinity chromatography column pre-equilibrated with buffer A (25). The column was washed with buffer A supplemented with KCl to the concentration of the pooled blue agarose fractions (typically 0.5 M KCl). IMPDH was eluted with 0.5 mM IMP in buffer A. Fractions containing IMPDH were pooled, dialyzed against buffer A overnight to remove IMP, and stored at ⫺20 °C (IMPDH activity ⫽ 1.4 ␮mol of product/min/mg). Protein concentrations were measured with the Bio-Rad assay using IgG as a standard. The final preparation was analyzed by 12% SDS-PAGE followed by Coomassie Blue staining, N-terminal sequencing by Edman degradation (Tufts

Medical School Protein Sequencing Facility), and MALDI-TOF mass spectrometry (University of Georgia Proteomics Resource facility). Gel Filtration Chromatography—Purified recombinant C. parvum IMPDH was applied to a 30-cm Sepharose 6 HR gel filtration column. The column was equilibrated and eluted with 50 mM Tris, pH 8, 100 mM KCl, and 3 mM EDTA at a flow rate of 0.5 ml/min. The column was calibrated with a mixture of thyroglobulin, ␥-globulin, ovalbumin, myoglobin, and vitamin B12 (molecular masses 670, 158, 44, 17, and 1.4 kDa, respectively; Bio-Rad). Enzyme Kinetics—IMPDH assays were performed in 100 mM KCl, 3 mM EDTA, 1 mM dithiothreitol, 50 mM Tris, pH 8.0 (assay buffer). Activity was routinely assayed in the presence of 250 ␮M IMP, 500 ␮M NAD, and 34 nM IMPDH at 25 °C. NADH production was monitored either by following absorbance change at 340 nm using a Hitachi U-2000 spectrophotometer (⑀ ⫽ 6.2 mM⫺1 cm⫺1) or by following fluorescence change on a BMG Labtechnologies Floustar Galaxy (excitation, 340 nm; emission, 460 nm). For crude extracts, the production of XMP was monitored by absorbance at 290 nm (⑀ ⫽ 5.4 mM⫺1 cm⫺1). The production of APADH and NHDH was followed at 363 nm (⑀ ⫽ 9.1 mM⫺1 cm⫺1) and 340 nm (⑀ ⫽ 6.2 mM⫺1 cm⫺1), respectively. The concentrations of IMP, NAD, and various analogs were varied. Using the SigmaPlot program (SPSS, Inc.), initial velocity data were fit to the Michaelis-Menten equation (Equation 1), the uncompetitive substrate inhibition equation (Equation 2), and the random Bi-Bi equation (Equation 3) as follows, v ⫽ V m关S兴/共Km ⫹ 关S兴兲

(Eq. 1)

Cryptosporidium IMPDH v ⫽ V m/共1 ⫹ K m/关S兴 ⫹ 关S兴/Kii兲

(Eq. 2)

v ⫽ V m关A兴关B兴/共K iaK b ⫹ K b关A兴 ⫹ K a关B兴 ⫹ 关A兴关B兴兲

(Eq. 3)

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where v represents the velocity, Vm is the maximal velocity, S is the substrate concentration, Km is the Michaelis constant, Kii is the intercept inhibition constant (26), A and B are substrates, Kia is the dissociation constant for A, and Ka and Kb are their respective Km values. The inhibition of C. parvum IMPDH by MPA, ␤CH2-TAD, and ADP was assayed at saturating IMP (250 ␮M) and varying concentrations of NAD (25–250 ␮M) and inhibitor (0.5 ␮M to 32 mM). The inhibition of IMPDH by GMP was monitored at fixed NAD (500 ␮M) and varying concentration of IMP (10 –100 ␮M) and inhibitor (0.5–1.5 mM). GMP inhibition was also measured at saturating IMP (250 ␮M) and varying concentration of NAD (25–250 ␮M) and inhibitor (0.5–1.5 mM). Data were fit to the following equations using the SigmaPlot program: the competitive inhibition equation (Equation 4), the uncompetitive inhibition equation (Equation 5), and the noncompetitive inhibition equation (Equation 6), v ⫽ V m关S兴/共Km共1 ⫹ 关I兴/Kis兲 ⫹ 关S兴兲

(Eq. 4)

v ⫽ V m关S兴/共Km ⫹ 关S兴共1 ⫹ 关I兴/Kii兲兲

(Eq. 5)

v ⫽ V m关S兴/共Km共1 ⫹ 关I兴/Kis兲 ⫹ 关S兴共1 ⫹ 关I兴/Kii兲兲

(Eq. 6)

where Kii and Kis represent the intercept and slope inhibition constants, respectively. Multiple inhibitor experiments with tiazofurin (1–9 mM) and ADP (4 –16 mM) were performed at 250 ␮M IMP and 250 ␮M NAD. Data were fit to the multiple inhibitor equation using the SigmaPlot program as follows, v ⫽ v 0/共1 ⫹ 关I兴/K i ⫹ 关J兴/K j ⫹ 关I兴关J兴/ ␣ K iK j兲

(Eq. 7)

where v0 represents the initial velocity in the absence of inhibitor, I is the inhibitor concentration of the first inhibitor for which Ki is the apparent inhibition constant, J is the concentration of the second inhibitor for which Kj is the apparent inhibition constant, and ␣ is the interaction constant. MZP is a slow tight binding inhibitor, so enzyme was preincubated with MZP in the absence of substrates. Complex formation was complete within 15 min, and the reaction was initiated with the addition of IMP (20 –100 ␮M) and NAD (500 ␮M) (15, 27). Varying IMP concentration had no effect on the extent of inhibition, which demonstrates that the E䡠MZP complex does not dissociate during the assay. The initial velocity data were fit to a simple binding model using Dynafit software (28). RESULTS

Expression and Purification of Recombinant C. parvum IMPDH—The goal of this study was to establish whether the prokaryotic origin of C. parvum IMPDH is reflected in its catalytic properties and to evaluate the potential for pathogenspecific inhibition. To generate sufficient amounts of enzyme for purification and biochemical characterization, the parasite gene was expressed in E. coli. The coding sequence of C. parvum IMPDH was amplified by PCR and introduced into a bacterial plasmid under control of the inducible TacTac promoter (23). The resulting construct was used to transform E. coli strain TX685 that lacks endogenous IMPDH activity due to a deletion in the GuaB locus (24). A complementation assay was performed to test whether the C. parvum enzyme expressed under these conditions is biologically active. TX685 bacteria grow well on rich LB medium but cannot proliferate on guanine-free minimal medium (Fig. 2A). Transformation with the plasmid expressing the C. parvum IMPDH restores growth of the mutant on minimal medium, demonstrating functional complementation (Fig. 2A). Furthermore, crude lysate prepared from liquid cultures of pTacCpIMPDH-transformed bacteria contained IMPDH activity absent from the mutant and control strain (data not shown). Initially, C. parvum IMPDH was purified from crude cell lysate by chromatography over Cibacron blue agarose followed by IMP affinity resin (see “Experimental Procedures” for de-

FIG. 3. Steady state kinetics of C. parvum IMPDH. A, plot of initial velocity versus IMP concentration at fixed NAD (500 ␮M). Data were fit by Equation 1, which describes Michaelis-Menten kinetics. B, plot of initial velocity versus NAD concentration at fixed IMP (250 ␮M). Data were fit by Equation 2, which describes uncompetitive substrate inhibition. C, 1/v versus 1/[IMP] plot. IMP and NAD concentrations were varied. Closed circles, 23 ␮M NAD; open circles, 45 ␮M NAD; open circles, 91 ␮M NAD; open triangles, 227 ␮M NAD. Velocity (v) is in arbitrary units. Assays were performed under standard conditions.

tails). Fractions containing enzymatic activity were analyzed by SDS-PAGE. As shown in Fig. 2B, the final preparation contained a single homogenous protein band with an apparent molecular mass of 43 kDa. The experiments that follow utilized enzyme purified by this protocol. Subsequently, IMP affinity chromatography alone was found to be sufficient for isolation of ⬎90% homogeneous enzyme with equivalent specific activity in 32% yield. We obtained 14 mg of purified IMPDH from a 2 liters culture using this streamlined protocol. The identity of the purified protein was confirmed by Nterminal sequencing. The sequence Gly-Thr-Lys-Asn-Ile-GlyLys-Gly-Leu-Thr established by Edman degradation corresponds to the predicted N-terminal sequence of C. parvum IMPDH after posttranslational removal of the initial methio-

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TABLE I Comparison of the kinetic parameters of C. parvum, human, and E. coli IMPDHs The varied substrate is shown in the parentheses. All C. parvum assays were performed in 50 mM Tris, pH 8.0, 1 mM dithiothreitol, 3 mM EDTA, 100 mM KCl, 25 °C. C, competitive; UC, uncompetitive; NC, noncompetitive; ND, no data. Parameter

C. parvum

kcat (s⫺1) Km(IMP) (␮M) Km(NAD) (␮M) Kii(NAD) (mM) Kis(GMP) (␮M) (C, IMP) Kis(MZP) (nM) (C, IMP) Kii(MPA) (nM) (UC, NAD) Kii(CH2-TAD) (nM) (UC, NAD) Ki(ADP) (mM) (NAD) Ki(tiazofurin) (mM) (NAD) ␣

3.3 ⫾ 0.2 29 ⫾ 3 150 ⫾ 20 2.9 ⫾ 0.7 46 ⫾ 3 11 ⫾ 3 9300 ⫾ 300 600 ⫾ 40 42 ⫾ 6 (NC) 1.5 ⫾ 0.1g 0.2 ⫾ 0.04

Human type 2

Human type 1

E. coli

0.4a 4a 6a 0.59a 100d 3.9b 6b 60e 8.8 (C)e 1.3 (NC)e 1.3 ⫾ 0.3e

1.8b 14b 42b ND 100d 8.2b 11b 95b ND ND ND

13c 61c 2000c 2.8c 86c 0.5c ⱖ10,000f 8500c ND ND ND

a

See Ref. 12; assays performed at 25 °C. See Ref. 30; assays performed at 37 °C. See Ref. 15; assays performed at 25 °C. d See Ref. 32; isozyme undetermined. e See Ref. 35; assays performed at 25 °C. f See Refs. 20 and 34. g Apparent Ki at 250 ␮M IMP and 250 ␮M NAD. b c

TABLE II The reaction of recombinant C. parvum IMPDH with NAD analogs Assay conditions are described in detail under “Experimental Procedures.” C. parvum Dinucleotide

Reduction potential Km

a b

kcat

kcat/Km

V

␮M

s⫺1

NAD

⫺0.320

110 ⫾ 20

1.6 ⫾ 0.3

(1.5 ⫾ 0.3) ⫻ 104

(6.5 ⫾ 0.5) ⫻ 104

APAD

⫺0.258

175 ⫾ 4

1.4 ⫾ 0.1

(8.2 ⫾ 0.2) ⫻ 103

(2.1 ⫾ 0.2) ⫻ 104

NHD

⫺0.320

ⱖ62,000

b

ⱖ0.2

M

b

⫺1

s⫺1

Human type 2a kcat/Km

2.3 ⫾ 0.2

M

⫺1

s⫺1

(5.7 ⫾ 0.9) ⫻ 102

Values for the human enzyme from Ref. 12. No saturation observed at 24 mM NHD.

nine. MALDI-TOF mass spectrometry detected a single molecular species with a molecular mass of 42,904 Da (Fig. 2C), which is in good agreement with the predicted size of the recombinant protein of 42,950 Da calculated using the ExPASy-ProtParam tool. Finally, the purified enzyme eluted as a single peak in close proximity to the 158-kDa standard during gel filtration chromatography, indicating that the active enzyme is a homotetramer, as previously reported for IMPDH enzymes from other organisms (Fig. 2D) (20). Steady State Kinetic Parameters—Initial velocity data were collected under standard assay conditions (see “Experimental Procedures”). The initial velocity versus varying concentrations of IMP at fixed NAD (500 ␮M) is well described by the Michaelis-Menten equation (Equation 1), with values of Km ⫽ 20 ⫾ 3 ␮M and kcat ⫽ 1.3 ⫾ 0.2 s⫺1 (Fig. 3A). In contrast, substrate inhibition is observed when varying the concentration of NAD at a fixed saturating IMP (250 ␮M; Fig. 3B). This NAD inhibition is commonly observed in IMPDH and is attributed to the formation of an E-XMP*䡠NAD complex (11). The data were fit to an equation describing uncompetitive substrate inhibition (Equation 2) (11, 21). The apparent value of Km for NAD is 110 ⫾ 20 ␮M, kcat ⫽ 1.6 ⫾ 0.3 s⫺1, and the value of Kii is 2.9 ⫾ 0.7 mM. To further probe the kinetic mechanism of C. parvum IMPDH, initial velocity was measured at varying concentrations of IMP and varying fixed concentrations of NAD. The concentrations of NAD were less than 0.1 ⫻ Kii so that substrate inhibition would be negligible. The double reciprocal plot displayed an intersecting line pattern indicating formation of an E䡠IMP䡠NAD complex (Fig. 3C). The data were fit to an equation describing a random addition of substrates (Equation 3): kcat ⫽ 3.3 ⫾ 0.2 s⫺1, Km(IMP) ⫽ 29 ⫾ 3 ␮M, Km(NAD) ⫽ 150 ⫾ 20 ␮M, in good agreement with the preliminary experiments

described above. These values are significantly different from the kinetic parameters of the human isozymes (Table I), demonstrating that the active site of the parasite enzyme is functionally different from the human enzymes. Probing the Mechanism of C. parvum IMPDH with NAD Analogs—APAD is a good substrate for C. parvum IMPDH, as is observed for IMPDHs from most organisms. At saturating IMP concentrations (250 ␮M), the initial velocity versus APAD data are well described by the Michaelis-Menten equation (data not shown) with values of Km(APAD) ⫽ 175 ␮M and kcat ⫽ 1.4 s⫺1 (Table II). This value is very similar to the value of kcat for the reaction with NAD determined under similar conditions (see above). APAD has a much higher reduction potential than NAD, so the rate of the hydride transfer step should be much faster than for NAD. Since the value of kcat is the same for the reactions of APAD and NAD, hydride transfer is not the ratelimiting step in the reaction of C. parvum IMPDH. Likewise, the similarity of the values of kcat for the two dinucleotides suggests that the rate of NADH release is not rate-limiting, since this rate should be different for reduced APADH. Therefore, the hydrolysis of E-XMP* is the most likely rate-limiting step (11, 12, 29). In contrast to APAD, NHD is a poor substrate for C. parvum IMPDH. No saturation was observed in the initial velocity versus NHD plot (maximum concentration ⫽ 24 mM), so only lower limits for the values of Km and kcat are reported (Table II). Nevertheless, the value of kcat/Km is determined with good precision, and is less than that of NAD by a factor of ⬃104. In contrast, the ratio of kcat/Km values for the human type 2 isozyme is ⬃100 (12). Since both NHD and NAD contain nicotinamide and therefore have identical reduction potentials, the difference in the ratio of kcat/Km values must derive from the binding specificities of the adenosine subsites. This observation


FIG. 4. Inhibition of C. parvum IMPDH. A, MPA inhibition of C. parvum IMPDH; 1/v versus 1/[NAD] plot. The concentration of IMP was 200 ␮M; NAD concentration was varied. Closed circles, no MPA; open circles, 12.8 ␮M MPA. B, multiple inhibition by Tiazofurin and ADP. IMP and NAD concentration were each 250 ␮M. Closed circles, No ADP; open circles, 8 mM ADP; closed squares, 16 mM ADP. Velocity (v) is in arbitrary units. Assays were performed under standard conditions.

indicates that the adenosine subsites are functionally very different in the parasite and human enzymes. Inhibitor Sensitivity of C. parvum IMPDH—In order to further identify functional differences in the active sites of C. parvum and human IMPDHs, we measured the sensitivity of the C. parvum enzyme to several known IMPDH inhibitors. We have tabulated our results together with literature values for the human isozymes and E. coli IMPDH (Table I). IMP analogs are competitive inhibitors of IMPDH with respect to IMP and noncompetitive with respect to NAD, as expected for a kinetic mechanism wherein substrate addition is random. Similar patterns are observed for C. parvum IMPDH. GMP is a competitive inhibitor of C. parvum IMPDH with respect to IMP (Ki ⫽ 46 ⫾ 3 ␮M) and noncompetitive with respect to NAD (Ki ⫽ 1100 ⫾ 30 ␮M). The Ki values are similar to those reported for other IMPDHs. A second IMP analog, MZP, also displays similar affinity for the parasite and human enzymes. MZP is a slow, tight binding inhibitor of IMPDH (30, 31). MZP was preincubated with C. parvum IMPDH and diluted into assay buffer containing IMP and NAD (see “Experimental Procedures”). Activity was constant during the measurement, and no dependence on IMP concentration was observed, indicating that the E䡠MZP complex does not dissociate upon dilution. Inhibition was complete within 15 min of preincubation. Using remaining activity as a measure of free enzyme, Kis ⫽ 11 nM for C. parvum IMPDH versus 8.2 and 3.9

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nM for type 1 and 2, respectively (Table II) (30). These observations indicate that the IMP binding sites of the parasite and human enzymes are functionally similar. The inhibition of IMPDH by NAD analogs is more complicated. Competitive, noncompetitive, or uncompetitive inhibition is observed versus NAD, depending on the relative affinity of a given NAD analog for the E䡠IMP and/or E-XMP* complexes. In C. parvum IMPDH, MPA is an uncompetitive inhibitor with respect to NAD, which indicates that MPA binds selectively to E-XMP*, as is observed with other IMPDHs (Fig. 4A). The value of Kii ⫽ 9.3 ␮M is 1000-fold greater than that for mammalian IMPDHs, and is typical of microbial IMPDHs (Table I) (21, 22, 33, 34). ␤-CH2-TAD, a nonhydrolyzable analog of TAD, is also an uncompetitive inhibitor of C. parvum IMPDH with respect to NAD. The value of Kii is 0.6 ␮M, which is 10-fold greater than the Ki for the human enzyme (30, 35). ADP is a noncompetitive inhibitor with respect to both IMP (Ki ⫽ 54 ⫾ 2 ␮M) and NAD (Ki ⫽ 42 ⫾ 6 ␮M) for the C. parvum enzyme, suggesting that ADP binds to both E䡠IMP and E-XMP*. In contrast, ADP is a competitive inhibitor versus NAD for human IMPDH, which indicates a strong preference for the E䡠IMP complex (35). These observations further demonstrate that the NAD site of C. parvum IMDPH is functionally different from the human isozymes. Multiple Inhibitor Experiments—Tiazofurin binds in the nicotinamide half of the NAD site, whereas ADP binds in the adenosine half (36). When used individually, both of these compounds are very weak inhibitors of C. parvum IMPDH (Table I). Fig. 4B shows that the presence of tiazofurin greatly increased the potency of ADP inhibition, with an interaction constant ␣ ⫽ 0.2. This observation indicates that tiazofurin induces a conformational change that favors ADP binding. In contrast, the presence of tiazofurin has no effect on ADP inhibition of human IMPDH, with an ␣ ⫽ 1.3, which suggests that the human enzyme does not undergo this conformational change (35). These data indicate that the dynamic properties of the NAD site in C. parvum IMPDH are also different from the human isozymes. DISCUSSION

C. parvum has lost the capability to synthesize both purines and pyrimidines nucleotides de novo and is entirely dependent on the metabolism of its host for these nucleic acid precursors (5). Inhibition of the salvage pathways consequently has strong effects on parasite growth, suggesting that the key salvage enzymes should be promising drug targets (5, 37). Two of these enzymes, thymidine kinase and IMPDH, were acquired through horizontal gene transfer from a eubacterium (5, 17). This divergent prokaryotic origin could aid the development of parasite-specific inhibitors. We have expressed and purified C. parvum IMPDH to establish whether the divergent phylogeny is reflected in the biochemistry of the enzyme and have identified similarities as well as pronounced differences between parasite and human IMPDH that provide important guidance for drug development. C. parvum IMPDH displays structural and kinetic properties typical of IMPDHs in general. The enzyme is a tetramer. High concentrations of NAD inhibit the reaction, consistent with a mechanism wherein IMP and NAD bind randomly and NADH dissociates before hydrolysis of E-XMP*, as is established in the human, Tritrichomonas foetus, and E. coli enzymes (11–13, 15). The inhibition patterns are also consistent with this mechanism, although we cannot eliminate an alternative mechanism where IMP binds first, because we have been unable to identify a competitive inhibitor with respect to NAD. Last, the values of kcat for C. parvum IMPDH for the reactions with NAD and APAD are comparable, suggesting that the rate-limiting

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FIG. 5. Multiple sequence alignments of C. parvum IMPDH with prokaryotic and eukaryotic enzymes. Bb, Borrelia burgdorferi; Ec, E. coli; Cp, C. parvum; Tf, T. foetus; H2, human IMPDH type 2. The residues that contact substrates and/or inhibitors in the solved structures of the human (42) or T. foetus (16) enzymes are underlined. Positions of critical residues are highlighted in the schematic representation of the active site in the top left panel. Thr45 and Gln469 (human type 2 numbering) contact the ribose of adenosine portion of NAD. His253 and Phe282 stack with the adenine ring of NAD. Asp364 interacts with the ribose of IMP, and Cys331 forms the covalent intermediate E-XMP*. Gln441 and Arg322 contact the nicotinamide portion of NAD and MPA. Arg429 and Tyr430 are part of the flap that folds into the vacant NADH site for the hydrolysis of E-XMP* (see Fig. 1D). Residues conserved among all sequences are highlighted in black, whereas those shared between C. parvum and the bacterial sequences but divergent from the human enzyme are shown in gray. Note the conservation in the IMP site but pronounced divergence between C. parvum (and bacterial IMPDHs) and the human enzyme in the NAD binding site and flap.

step does not involve the dinucleotide and therefore cannot be hydride transfer or NADH release. These observations suggest that the hydrolysis of E-XMP* is rate-limiting, as observed for the human, T. foetus, and E. coli enzymes (11–13, 15). Whereas the above properties appear to be common to all IMPDHs, the bacterial and mammalian enzymes have several distinctive functional characteristics (Table I). First, the values of Km are generally higher for bacterial IMPDHs, with the value of Km(NAD) typically 1–2 mM versus a maximum of 40 ␮M for the human enzymes (12, 15, 21, 30, 38, 39). The values of kcat also tend to be higher, ranging from 2 to 24 s⫺1 versus a maximum of 2 s⫺1 for the human enzymes. The values of kcat and Km for C. parvum IMPDH, while clearly higher than the human isozymes, are rather low for a bacterial IMPDH. This may reflect the further evolution of the transferred gene to optimize function in its new context. The C. parvum enzyme has retained resistance to MPA, which is clearly a bacterial characteristic (see Table I). Thus, the functional properties of C. parvum IMPDH generally reflect its prokaryotic origin. C. parvum IMPDH displays several differences from the human isozymes that might be exploited for drug design. The most dramatic differences are associated with the NAD site, including the value of Km for NAD, the value of Kii for NAD inhibition, the specificity for NAD versus NHD, and the values of Kii for MPA and ␤CH2-TAD inhibition (Tables I and II). These data are consistent with the comparison of the primary sequences of C. parvum and human IMPDH. In human IMPDH, the adenine ring of NAD is sandwiched between His253 and Phe282, whereas Thr45 and Gln469 from the adjacent subunit form hydrogen bonds to N1 of adenine and ribosyl hydroxyls, respectively (40). None of these residues are conserved in C. parvum IMPDH (see Fig. 5). C. parvum IMPDH also contains substitutions at the nicotinamide end of the NAD site, with Lys and Glu substituting for Arg322 and Gln441. Taken together, these data suggest the NAD binding site as the most suitable target for the development of C. parvum-specific inhibitors.

Drug selectivity is also determined by dynamic conformational changes within the dinucleotide site (31, 41). MPA binds to the vacant NADH site of the E-XMP* intermediate and blocks the movement of the flap required for the hydrolysis reaction (Fig. 1D). Therefore, the equilibrium between open and closed conformations determines MPA selectivity. This equilibrium can be assessed by monitoring the interaction of two inhibitors, tiazofurin and ADP. Tiazofurin binds in the nicotinamide portion of the NAD site, whereas ADP binds in the adenosine portion. If the open conformation is favored, as in the human type 2 isozyme, the two inhibitors bind independently, as demonstrated by the interaction constant ␣ ⬃ 1. However, if the closed conformation is favored as in the T. foetus enzyme, the binding of the first inhibitor opens a binding site for the second and a synergistic interaction is observed (␣ ⫽ 0.02) (35). Tiazofurin and ADP also interact synergistically in the C. parvum enzyme, which indicates that the closed conformation is favored in this enzyme. It is likely that dynamic conformational changes also play a role in the inhibitor selectivity of the IMP site. MZP induces the closed flap conformation in T. foetus IMPDH as well as movement in the loop that contains the catalytic Cys (41). MZP probably induces a similar conformation in human IMPDH (a similar conformation is induced by the related inhibitor ribavirin monophosphate) (42). However, more binding energy must be expended to induce the closed conformation in human IMPDH, since this enzyme favors the open conformation. This unfavorable dynamic equilibrium can explain the lower affinity of MZP for the human enzyme (Kis ⬃ 4 nM for human type 2 versus 0.15 nM for T. foetus IMPDH). This reasoning suggests that MZP will be a more potent inhibitor of the C. parvum enzyme than the human enzyme, but this is not observed. Perhaps the dynamics of the loop that contains the active site Cys account for this puzzling result. The residues that form the IMP site are strongly conserved (Fig. 5), and the predominant interactions involve main chain hydrogen bonds to relatively rigid protein segments. In con-

Cryptosporidium IMPDH trast, the loop that contains the catalytic Cys is highly dynamic. This loop undergoes hinged rigid body motion but can also assume several conformations (40, 43). Clearly, the mobility of this loop will also be a determinant of drug affinity. The sequence of this loop varies in prokaryotic and eukaryotic IMPDH, so it is reasonable to expect that the dynamic properties of this loop will also vary (Fig. 5). This hypothesis is supported by the varying extents of disorder in this loop in structures of IMPDHs from different sources (39, 43, 44). Whereas the mobile structural elements of IMPDH clearly complicate drug design, they also promise opportunity. These mobile elements are in or near regions of high sequence divergence; in particular, the flap is difficult to align due to the prevalence of sequence insertions and deletions. Obviously, the catalytically competent conformation of the active site must be similar for all IMPDHs. However, the disordered regions suggest that unique, and energetically accessible, alternative conformations must also exist. The challenge is to identify compounds that will bind to these conformations. Arkin and colleagues have recently exploited the conformational heterogeneity of IL-2 to inhibit cytokine-receptor interactions (45). We believe similar strategies can be utilized to develop parasite-specific inhibitors of IMPDH.

11. 12. 13. 14. 15. 16. 17.

Acknowledgments—We thank Satoshi Shuto and Akira Matsuda for providing MZP and Krzysztof W. Pankiewicz for providing ␤-methylene-TAD.

33.

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