Acid-base catalytic mechanism of dihydropyrimidinase from pH studies

Therapeutical Potential of Imines; Synthesis, Single Crystal Structure, Computational, Molecular Modeling, and ADMET Evaluation

Imines are multipurpose pharmacophores, simply accessible compounds, and have a broad range of usage in several areas of chemistry especially in medicine. Two novel compound imines, (E)-4-methyl-2-((o-tolylimino)methyl)phenol (1) and (E)-2-(((4-methoxybenzyl)imino)methyl)-4-methylphenol (2), were synthesized with effective product via reported protocol in the literature. Single crystal X-ray diffraction (SCXRD) was employed for structural exposition, disclosing that both compounds are orthorhombic. To optimize the newly designed imines, a B3LYP functional with a basis set 6-31G(d,p) was mainly considered. DFT results were utilized to check correlation between the data recovered from SCXRD outcomes and also to measure the energy difference. Hirshfeld surface study was done to demonstrate the intermolecular contacts along the percentage of interaction in the overall crystalline compound. Molecular operating environment program was tested against AChE and BChE enzymes to perform a modeling study of the compounds. The docking score and binding affinity of the compounds revealed that 2 showed comparatively more inhibition than 1. In silico ADMET studies exposed the physiochemical nature of these novel compounds, and it also unveiled that both compounds behaved as drug-like candidates.

Crystal structures of vertebrate dihydropyrimidinase and complexes from Tetraodon nigroviridis with lysine carbamylation: metal and structural requirements for post-translational modification and function

Lysine carbamylation, a post-translational modification, facilitates metal coordination for specific enzymatic activities. We have determined structures of the vertebrate dihydropyrimidinase from Tetraodon nigroviridis (TnDhp) in various states: the apoenzyme as well as two forms of the holoenzyme with one and two metals at the catalytic site. The essential active-site structural requirements have been identified for the possible existence of four metal-mediated stages of lysine carbamylation. Only one metal is sufficient for stabilizing lysine carbamylation; however, the post-translational lysine carbamylation facilitates additional metal coordination for the regulation of specific enzymatic activities through controlling the conformations of two dynamic loops, Ala(69)-Arg(74) and Met(158)-Met(165), located in the tunnel for the substrate entrance. The substrate/product tunnel is in the "open form" in the apo-TnDhp, in the "intermediate state" in the monometal TnDhp, and in the "closed form" in the dimetal TnDhp structure, respectively. Structural comparison also suggests that the C-terminal tail plays a role in the enzymatic function through interactions with the Ala(69)-Arg(74) dynamic loop. In addition, the structures of the dimetal TnDhp in complexes with hydantoin, N-carbamyl-β-alanine, and N-carbamyl-β-amino isobutyrate as well as apo-TnDhp in complex with a product analog, N-(2-acetamido)-iminodiacetic acid, have been determined. These structural results illustrate how a protein exploits unique lysines and the metal distribution to accomplish lysine carbamylation as well as subsequent enzymatic functions.

2-(2-{2-[2-(Dibromo-meth-yl)phen-oxy]eth-oxy}benz-yloxy)benzaldehyde

The mol­ecule of the title compound, C₂₃H₂₀Br₂O₄, adopts a Z conformation as a result of inter­molecular C—H⋯Br bonding. One benzene ring, with the structure R-CHBr₂, makes a dihedral angle of 63.0 (2)° with the other benzene ring attached to the aldehyde group. Inter­molecular π–π stacking inter­actions [centroid–centroid distance = 3.698 (4) Å] and a weak C—H⋯Br contact is present in the crystal structure.

Dihydropyrimidinase deficiency: Phenotype, genotype and structural consequences in 17 patients

Dihydropyrimidinase (DHP) is the second enzyme of the pyrimidine degradation pathway and catalyses the ring opening of 5,6-dihydrouracil and 5,6-dihydrothymine. To date, only 11 individuals have been reported suffering from a complete DHP deficiency. Here, we report on the clinical, biochemical and molecular findings of 17 newly identified DHP deficient patients as well as the analysis of the mutations in a three-dimensional framework. Patients presented mainly with neurological and gastrointestinal abnormalities and markedly elevated levels of 5,6-dihydrouracil and 5,6-dihydrothymine in plasma, cerebrospinal fluid and urine. Analysis of DPYS, encoding DHP, showed nine missense mutations, two nonsense mutations, two deletions and one splice-site mutation. Seventy-one percent of the mutations were located at exons 5-8, representing 41% of the coding sequence. Heterologous expression of 11 mutant enzymes in Escherichia coli showed that all but two missense mutations yielded mutant DHP proteins without significant activity. Only DHP enzymes containing the mutations p.R302Q and p.T343A possessed a residual activity of 3.9% and 49%, respectively. The crystal structure of human DHP indicated that the point mutations p.R490C, p.R302Q and p.V364M affect the oligomerization of the enzyme. In contrast, p.M70T, p.D81G, p.L337P and p.T343A affect regions near the di-zinc centre and the substrate binding site. The p.S379R and p.L7V mutations were likely to cause structural destabilization and protein misfolding. Four mutations were identified in multiple unrelated DHP patients, indicating that DHP deficiency may be more common than anticipated.

Quantitative analysis and functional evaluation of zinc ion in the D-hydantoinase from Pseudomonas putida YZ-26

D-hydantoinase (HDT) is a metal-dependent enzyme that is widely used in industrial bioconversion to D-amino acids as valuable intermediates in the fields of food, pharmaceutical industry and agriculture. In this report, we prepared apo-HDT (metal-removed HDT) and Zn(2+)-HDT (Zn(2+)-added HDT) in vitro from a recombinant HDT (re-HDT) expressed in E. coli. The Zn(2+)-HDT and re-HDT contain 2.17 and 0.95 mol Zn(2+) per mol subunit, respectively, and they have comparable enzymatic activities. In contrast, the apo-HDT only retains 0.04 mol Zn(2+) per mol subunit with less than 10% activity, compared with the re-HDT. When the apo-HDT was reconstituted with ZnCl(2), the enzymatic activity recovery was about 75%. Moreover, the fluorescence intensity, circular dichroism spectra and thermo-stability of the apo-HDT and Zn(2+)-HDT are quite different from those of the re-HDT. These data suggest that the re-HDT may have two Zn(2+)-binding sites, one is an intrinsic or tight-binding site (zinc-alpha) essential for its activity and the other is a vacant or loose-binding site (zinc-beta) possibly non-essential for the activity.

Amidohydrolases of the reductive pyrimidine catabolic pathway purification, characterization, structure, reaction mechanisms and enzyme deficiency

In the reductive pyrimidine catabolic pathway uracil and thymine are converted to beta-alanine and beta-aminoisobutyrate. The amidohydrolases of this pathway are responsible for both the ring opening of dihydrouracil and dihydrothymine (dihydropyrimidine amidohydrolase) and the hydrolysis of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyrate (beta-alanine synthase). The review summarizes what is known about the properties, kinetic parameters, three-dimensional structures and reaction mechanisms of these proteins. The two amidohydrolases of the reductive pyrimidine catabolic pathway have unrelated folds, with dihydropyrimidine amidohydrolase belonging to the amidohydrolase superfamily while the beta-alanine synthase from higher eukaryotes belongs to the nitrilase superfamily. beta-Alanine synthase from Saccharomyces kluyveri is an exception to the rule and belongs to the Acyl/M20 family.

Clinical, biochemical and genetic findings in two siblings with a dihydropyrimidinase deficiency

Dihydropyrimidinase (DHP) is the second enzyme of the pyrimidine degradation pathway and it catalyses the ring opening of 5,6-dihydrouracil and 5,6-dihydrothymine to N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyric acid, respectively. To date, only nine individuals have been reported suffering from a complete DHP deficiency. We report two siblings presenting with strongly elevated levels of 5,6-dihydrouracil and 5,6-dihydrothymine in plasma, cerebrospinal fluid and urine. One of the siblings had a severe delay in speech development and white matter abnormalities, whereas the other one was free of symptoms. Analysis of the DHP gene (DPYS) showed that both patients were compound heterozygous for the missense mutation 1078T>C (W360R) in exon 6 and a novel missense mutation 1235G>T (R412M) in exon 7. Heterologous expression of the mutant enzymes in Escherichia coli showed that both missense mutations resulted in a mutant DHP enzyme without residual activity. Analysis of the crystal structure of eukaryotic DHP from the yeast Saccharomyces kluyveri and the slime mold Dictyostelium discoideum suggests that the W360R and R412M mutations lead to structural instability of the enzyme which could potentially impair the assembly of the tetramer.

The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity

In eukaryotes, dihydropyrimidinase catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Here we describe the three-dimensional structures of dihydropyrimidinase from two eukaryotes, the yeast Saccharomyces kluyveri and the slime mold Dictyostelium discoideum, determined and refined to 2.4 and 2.05 angstroms, respectively. Both enzymes have a (beta/alpha)8-barrel structural core embedding the catalytic di-zinc center, which is accompanied by a smaller beta-sandwich domain. Despite loop-forming insertions in the sequence of the yeast enzyme, the overall structures and architectures of the active sites of the dihydropyrimidinases are strikingly similar to each other, as well as to those of hydantoinases, dihydroorotases, and other members of the amidohydrolase superfamily of enzymes. However, formation of the physiologically relevant tetramer shows subtle but nonetheless significant differences. The extension of one of the sheets of the beta-sandwich domain across a subunit-subunit interface in yeast dihydropyrimidinase underlines its closer evolutionary relationship to hydantoinases, whereas the slime mold enzyme shows higher similarity to the noncatalytic collapsin-response mediator proteins involved in neuron development. Catalysis is expected to follow a dihydroorotase-like mechanism but in the opposite direction and with a different substrate. Complexes with dihydrouracil and N-carbamyl-beta-alanine obtained for the yeast dihydropyrimidinase reveal the mode of substrate and product binding and allow conclusions about what determines substrate specificity, stereoselectivity, and the reaction direction among cyclic amidohydrolases.

Purification, crystallization and X-ray diffraction analysis of dihydropyrimidinase from Dictyostelium discoideum

Dihydropyrimidinase (EC 3.5.2.2) is the second enzyme in the reductive pyrimidine-degradation pathway and catalyses the hydrolysis of 5,6-dihydrouracil and 5,6-dihydrothymine to the corresponding N-carbamylated beta-amino acids. The recombinant enzyme from the slime mould Dictyostelium discoideum was overexpressed, purified and crystallized by the vapour-diffusion method. One crystal diffracted to better than 1.8 A resolution on a synchrotron source and was shown to belong to space group I222, with unit-cell parameters a = 84.6, b = 89.6, c = 134.9 A and one molecule in the asymmetric unit.

Phylogenetic Analysis and Biochemical Characterization of a Thermostable Dihydropyrimidinase from Alkaliphilic Bacillus sp. TS-23

Two degenerate primers established from the alignment of highly conserved amino acid sequences of bacterial dihydropyrimidinases (DHPs) were used to amplify a 330-bp gene fragment from the genomic DNA of Bacillus sp. TS-23 and the amplified DNA was successfully used as a probe to clone a dhp gene from the strain. The open reading frame of the gene consisted of 1422 bp and was deduced to contain 472 amino acids with a molecular mass of 52 kDa. The deduced amino acid sequence exhibited greater than 45% identity with that of prokaryotic D-hydantoinases and eukaryotic DHPs. Phylogenetic analysis showed that Bacillus sp. TS-23 DHP is grouped together with Bacillus stearothermophilus D-hydantoinase and related to dihydroorotases and allantoinases from various organisms. His6-tagged DHP was over-expressed in Escherichia coli and purified by immobilized metal affinity chromatography to a specific activity of 3.46 U mg(-1) protein. The optimal pH and temperature for the purified enzyme were 8.0 and 60 degrees C, respectively. The half-life of His6-tagged DHP was 25 days at 50 degrees C. The enzyme activity was stimulated by Co2+ and Mn2+ ions. His6-tagged DHP was most active toward dihydrouracil followed by hydantoin derivatives. The catalytic efficiencies (kcat/Km) of the enzyme for dihydrouracil and hydantoin were 2.58 and 0.61 s(-1) mM(-1), respectively.

Discovery of a novel N-iminylamidase activity: substrate specificity, chemicoselectivity and catalytic mechanism

Enzymatic hydrolysis of the N-iminylamide was investigated in this study. An enzyme possessing N-iminylamidase activity from pig liver was purified to electrophoretic homogeneity. This enzyme was also active, however, with imides and appears to be identical to pig liver imidase. The identification was confirmed by copurification of enzyme activities and by specificities of typical substrates of mammalian imidase, such as phthalimide, dihydrouracil, and maleimide. The hydrolysis of 3-iminoisoindolinone was further analyzed by HPLC, (13)C NMR spectrometry, and LC-MS measurements to determine its chemicoselectivity. All data indicated that this enzyme chemicoselectively catalyzed the hydrolysis of the N-iminylamide to produce the compound bearing the diamine and carboxylate group. The pH profiles of this enzyme suggest that one of the protons of 3-iminoisoindolinone was important to promote the ring-opening process of this substrate. These results constituted a first study on the enzymatic hydrolysis of compounds bearing the N-iminylamide functional group.

A novel cold-adapted imidase from fish Oreochromis niloticus that catalyzes hydrolysis of maleimide

In this paper we report the first comparative study of cold-adapted imidase (EC 3.5.2.2) from the fish (Oreochromis niloticus) liver and its thermophilic counterparts taken from pig liver and Escherichia coli (overexpressed recombinant hydantoinase from Agrobacterium radiobacter NRRL B1). Approximately 6000-fold purification and a 40% yield of fish imidase activity were obtained through ammonium sulfate precipitation, octyl, chelating, DEAE, and hydroxyapatite chromatography. This cold-adapted imidase was characterized by a specific activity 10- to a 100-fold higher than those of its thermophilic counterparts below room temperature (25 degrees C or lower) conditions but less stable at elevated temperatures (40 degrees C or higher). A less organized helical structure (compared to those of pig liver and bacterial imidases) was observed by circular dichroism. Furthermore, maleimide was first identified as a novel substrate of all imidases examined, and confirmed by HPLC and NMR analysis. These results constituted a first study to discover a novel cold-adapted imidase with surprising high activity. These findings might be also helpful for industrial application of imidase.

Dihydropyrimidine amidohydrolases and dihydroorotases share the same origin and several enzymatic properties

Slime mold, plant and insect dihydropyrimidine amidohydrolases (DHPases, EC 3.5.2.2), which catalyze the second step of pyrimidine and several anti-cancer drug degradations, were cloned and shown to functionally replace a defective DHPase enzyme in the yeast Saccharomyces kluyveri. The yeast and slime mold DHPases were over-expressed, shown to contain two zinc ions, characterized for their properties and compared to those of the calf liver enzyme. In general, the kinetic parameters varied widely among the enzymes, the mammalian DHPase having the highest catalytic efficiency. The ring opening was catalyzed most efficiently at pH 8.0 and competitively inhibited by the reaction product, N-carbamyl-beta-alanine. At lower pH values DHPases catalyzed the reverse reaction, the closing of the ring. Apparently, eukaryote DHPases are enzymatically as well as phylogenetically related to the de novo biosynthetic dihydroorotase (DHOase) enzymes. Modeling studies showed that the position of the catalytically critical amino acid residues of bacterial DHOases and eukaryote DHPases overlap. Therefore, only a few modifications might have been necessary during evolution to convert the unspecialized enzyme into anabolic and catabolic ones.

The role of metal on imide hydrolysis: metal content and pH profiles of metal ion-replaced mammalian imidase

Imidase catalyzes the hydrolysis of a variety of imides. The removal of metal from imidase eliminates its activity but does not affect its tetrameric and secondary structure. The reactivation of the apoenzyme with transition metal ions Co(2+), Zn(2+), Mn(2+), and Cd(2+) shows that imidase activity is linearly dependent on the amount of metal ions added. Ni(2+) and Cu(2+) are also inserted, one per enzyme subunit, into the apoimidase, but do not restore imidase activity. Enzyme activity with different metal replaced imidase varies significantly. However, the changes of the metal contents do not appear to affect the pK(a)s obtained from the bell-shaped pH profiles of metal reconstituted imidase. The metal-hydroxide mechanism for imidase action is not supported based on the novel findings from this study. It is proposed that metal ion in mammalian imidase functions as a Lewis acid, which stabilizes the developing negative charge of imide substrate in transition state.

Identification, purification, and characterization of a thermophilic imidase from pig liver

This study investigates thermophilic imidase activity of the liver. We demonstrate that imidase catalyzes the hydrolysis of imides at a temperature substantially higher than that of its native environment. Then, a thermophilic imidase is purified to homogeneity from pig liver, and its thermoproperties are studied. About 2500-fold of purification and 15% yield of imidase activity are obtained after ammonium sulfate precipitation, octyl, DEAE, chelation, and gel filtration chromatography. While avoiding heat treatment for the protein purification, this study also indicates that only one enzyme is responsible for the imidase activity. This homogenous enzyme prefers to catalyze hydrolysis of imides at above 60 degrees C rather than at the body temperature of a pig. Although stable at below 50 degrees C, imidase quickly loses its activity at above 65 degrees C. Thus, the temperature effect on imidase activity is limited mainly by its thermostability. Substrate specificity of imidase is also temperature dependent. Our results demonstrate that the hydrolysis of physiological substrates is the most temperature dependent and that of hydantoins is the least temperature dependent. When increasing the reaction temperature from 25 to 60 degrees C, specific activities increase 50- and 60-fold for dihydrouracil and dihydrothymine, respectively. The temperature effect on the K(m) and V(max) of imidase is substrate dependent.

Purification of a D-hydantoinase using a laboratory-scale streamline phenyl column as the initial step

A D-hydantoinase from Thermus sp. was overexpressed in Escherichia coli and purified to homogeneity for subsequent crystallization. The purification was performed with hydrophobic interaction chromatography as the capture step followed by anion-exchange chromatography and gel permeation chromatography as intermediate purification and polishing steps, respectively. The hydrophobic interaction step was done in fluidized bed mode in a laboratory-scale Streamline column made from conventional laboratory equipment. The whole purification protocol could be finished within one day. The purified enzyme crystallizes. The crystals are suitable for X-ray protein structure analysis and diffract to at least 2.3 A resolution. Complete data sets have been measured up to 2.6 A resolution. The X-ray structure is currently being solved.

Radiochemical assay for determination of dihydropyrimidinase activity using reversed-phase high-performance liquid chromatography

A radiochemical assay was developed to measure the activity of dihydropyrimidinase (DHP) in human liver homogenates. The method is based on the separation of radiolabeled dihydrouracil from N-carbamyl-beta-alanine by HPLC with on-line detection of radioactivity combined with detection of 14CO2 by liquid scintillation counting. The assay was linear with time and protein concentration. The minimum amount of radiolabeled products which could be determined proved to be 12 pmol using a purified stock solution of [2-(14)C]-5,6-dihydrouracil. This highly sensitive assay is especially suitable to identify patients with a dihydropyrimidinase deficiency.

Identification of the structural similarity in the functionally related amidohydrolases acting on the cyclic amide ring

The functionally related amidohydrolases, including D-hydantoinases, dihydropyrimidinases, allantoinases and dihydro-orotases, share a similar catalytic function of acting on the cyclic amide ring. We aligned 16 amidohydrolases by taking account of the conservative substitution and found a number of highly conserved regions and invariant amino acid residues. Analyses of the secondary structure and hydropathy profile of the enzymes revealed a significant degree of similarity in the conserved regions. Among the regions, the long stretched region I is of particular interest, because it is mainly composed of invariant amino acid residues, showing a similarity of 69% for the enzymes. A search of the protein data bank using the sequence of the conserved region I identified a number of proteins possessing a similar catalytic property, providing a clue that this region might be linked with the catalytic function. As a particular sequence, one aspartic acid and four histidine residues are found to be rigidly conserved in the functionally related amidohydrolases. In order to investigate the significance of the conserved residues, site-directed mutagenesis was carried out typically for the D-hydantoinase gene cloned from Bacillus stearothermophilus SD1. These residues were found to be essential for metal binding as well as catalysis, strongly implying that these invariant residues play a critical role in other enzymes as well as in D-hydantoinase. On the basis of the similar catalytic function and existence of the rigidly conserved sequence, we propose a close evolutionary relationship among the functionally related amido hydrolases, including D-hydantoinase, dihydropyrimidinase, allantoinase and dihydroorotase.

Purification and characterization of thermostable D-hydantoinase from thermophilic Bacillus stearothermophilus SD-1

A thermostable D-hydantoinase of thermophilic Bacillus stearothermophilus SD-1 was purified to homogeneity using an immuno-affinity chromatography. The affinity chromatography that employed polyclonal antibody immobilized on Sepharose 4B was simple to operate and gave a purification yield of 60% of enzyme activity. Molecular mass of the enzyme was determined to be about 133.9 kDa by gel filtration chromatography and the molecular mass of the subunit was 54 kDa on SDS-PAGE. Mass spectrometric analyses were also performed for the determination of the molecular mass of the native enzyme and its subunit. The apparent molecular masses were 51.1 and 102.1 kDa for the subunit and native enzyme, respectively. Based on the molecular masses determined by these two methods, it is suggested that the D-hydantoinase exists as a dimeric conformation in the cell. Isoelectric pH of the enzyme was observed to be 4.47. It was found that the enzyme requires one manganese ion per molecule of enzyme for the activity. The optimal pH and temperature for the catalytic activity were about 8.0 and 65 degrees C, respectively. The half-life of the enzyme was estimated to be 30 min at 80 degrees C, confirming that the enzyme purified is one of the most thermostable D-hydantoinase reported so far. Kinetic constants of the enzyme for different substrates were also determined.

(R)-5-fluoro-5,6-dihydrouracil: kinetics of oxidation by dihydropyrimidine dehydrogenase and hydrolysis by dihydropyrimidine aminohydrolase

The biologically active isomer of 5-fluoro-5,6-dihydrouracil [(R)-5-fluoro-5,6-dihydrouracil, R-FUH2] was synthesized to study the kinetics of its enzymatic oxidation and hydrolysis by homogeneous dihydropyrimidine dehydrogenase (DPDase) and dihydropyrimidine aminohydrolase (DPHase), respectively. DPDase catalyzed the slow oxidation of R-FUH2 at pH 8 and 37 degrees with a Km of 210 microM and a kcat of 0.026 sec-1 at a saturating concentration of NADP+. The catalytic efficiency (kcat/Km) of DPDase for R-FUH2 was 1/14th of that for 5,6-dihydrouracil (UH2). In the opposite direction, DPDase catalyzed the reduction of 5-fluorouracil (FU) with a Km of 0.70 microM and a kcat of 3 sec-1 at a saturating concentration of NADPH. Thus, DPDase catalyzed the reduction of FU 30,000-fold more efficiently than the oxidation of R-FUH2. In contrast to the slow oxidation of R-FUH2 by DPDase, R-FUH2 was hydrolyzed very efficiently by DPHase with a Km of 130 microM and a kcat of 126 sec-1. The catalytic efficiency of DPHase for the hydrolysis of R-FUH2 was approximately twice that for the hydrolysis of UH2. Because R-FUH2 is hydrolysis of R-FUH2 was approximately twice that for the hydrolysis of UH2. Because R-FUH2 is hydrolyzed considerably more efficiently than it is oxidized and because the activity of DPHase was 250- to 500-fold greater than that of DPDase in bovine and rat liver, the hydrolytic pathway should predominate in vivo.

Purification, characterization and inhibition of dihydropyrimidinase from rat liver

Dihydropyrimidinase (DHPase) was purified 564-fold over the initial rat liver extract, using heat, ammonium sulfate fractionation, DEAE-Sepharose CL-6B, carboxymethyl-Sepharose CL-6B, hydroxyapatite and Sephacryl S-300 chromatography. The purified enzyme was shown to be homogeneous by gel electrophoresis both in the presence and absence of SDS. Its molecular mass, determined by gel filtration, was 215 kDa and the subunit mass was 54 kDa. DHPase catalyzed the reversible cyclization of 5,6-dihydrouracil (H2Ura) to N-carbamoyl-beta-alanine or 5,6-dihydrothymine (H2Thy) to N-carbamoyl-beta-aminoisobutyric acid. Authentic 5-bromo-5,6-dihydrouracil (BrH2Ura) and commercially available H2Thy were racemic. However, these 5-substituted 5,6-dihydropyrimidines were hydrolyzed by over 96% and 98%, respectively, by DHPase. These results suggest that dihydropyrimidinase has no stereo specificities for 5-substituents of H2Ura. The addition of H2Ura and H2Thy competitively inhibited the enzyme activity against BrH2Ura. However, the addition of N-carbamoyl-beta-alanine or N-carbamoyl-beta-amino-isobutyric acid showed hyperbolic mixed-type inhibition, when BrH2Ura was used as the substrate. The values of the dissociation constants of BrH2Ura, N-carbamoyl-beta-alanine and N-carbamoyl-beta-aminoisobutyric acid were 17 microM, 0.38 mM and 0.38 mM, respectively. DHPase from the rat liver contains 4 mol Zn2+/mol active enzyme, presumably one atom/subunit. Zn2+ also inhibited the hydrolysis of BrH2Ura by the enzyme. The Ki for Zn2+ as an inhibitor of DHPase was 23 microM, and the maximum rate of inactivation was 0.057 min-1 at 37 degrees C. H2Ura and H2Thy protected the enzyme activity from Zn2+ inactivation.