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1.
Int J Mol Sci ; 22(18)2021 Sep 15.
Article in English | MEDLINE | ID: mdl-34576147

ABSTRACT

Drug-resistant Staphylococcus aureus is an imminent threat to public health, increasing the importance of drug discovery utilizing unexplored bacterial pathways and enzyme targets. De novo pyrimidine biosynthesis is a specialized, highly conserved pathway implicated in both the survival and virulence of several clinically relevant pathogens. Class I dihydroorotase (DHOase) is a separate and distinct enzyme present in gram positive bacteria (i.e., S. aureus, B. anthracis) that converts carbamoyl-aspartate (Ca-asp) to dihydroorotate (DHO)-an integral step in the de novo pyrimidine biosynthesis pathway. This study sets forth a high-throughput screening (HTS) of 3000 fragment compounds by a colorimetry-based enzymatic assay as a primary screen, identifying small molecule inhibitors of S. aureus DHOase (SaDHOase), followed by hit validation with a direct binding analysis using surface plasmon resonance (SPR). Competition SPR studies of six hit compounds and eight additional analogs with the substrate Ca-asp determined the best compound to be a competitive inhibitor with a KD value of 11 µM, which is 10-fold tighter than Ca-asp. Preliminary structure-activity relationship (SAR) provides the foundation for further structure-based antimicrobial inhibitor design against S. aureus.


Subject(s)
Dihydroorotase/antagonists & inhibitors , Enzyme Inhibitors/analysis , Enzyme Inhibitors/pharmacology , High-Throughput Screening Assays , Small Molecule Libraries/analysis , Small Molecule Libraries/pharmacology , Staphylococcus aureus/enzymology , Catalytic Domain , Dihydroorotase/chemistry , Dihydroorotase/isolation & purification , Dihydroorotase/metabolism , Enzyme Inhibitors/chemistry , Molecular Docking Simulation , Small Molecule Libraries/chemistry , Staphylococcus aureus/drug effects , Structure-Activity Relationship
2.
Protein Expr Purif ; 88(1): 98-106, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23246866

ABSTRACT

Staphylococcus aureus is a pathogenic bacterium that causes a variety of mild to lethal human diseases. The rapid spread of multidrug-resistant strains makes the discovery of new antimicrobial agents critical. Dihydroorotase (PyrC), the third enzyme in the bacterial pyrimidine biosynthesis pathway, is structurally and mechanistically distinct from its mammalian counterpart. It has been confirmed to be essential in S. aureus making it an attractive antibacterial drug target. No protocol to express and purify S. aureus PyrC (SaPyrC) has been reported. To obtain the SaPyrC enzyme and overcome anticipated solubility problems, the SaPyrC gene was cloned into the pET-SUMO vector. The N-terminal His-SUMO fused SaPyrC was expressed in Escherichia coli BL21 (DE3) with an HRV 3C protease recognition site inserted between the SUMO tag and SaPyrC to allow for improved cleavage by HRV protease. Purification of cleaved protein using HisTrap affinity and gel filtration columns resulted in native SaPyrC with estimated 95% purity and 40% yield. Both His-SUMO tagged and native SaPyrC form dimers, and enzyme characterization studies have shown that the His-SUMO tag affects enzyme activity slightly. Forward and reverse kinetic rate constants for both tagged and native SaPyrC were determined, and pH profiling studies revealed the optimal pH values for forward and reverse reactions.


Subject(s)
Dihydroorotase/genetics , Dihydroorotase/isolation & purification , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/isolation & purification , Staphylococcus aureus/enzymology , Anti-Bacterial Agents/isolation & purification , Anti-Bacterial Agents/metabolism , Cloning, Molecular , Dihydroorotase/biosynthesis , Drug Resistance, Multiple, Bacterial , Escherichia coli/genetics , Gene Expression , Genetic Vectors , Humans , Recombinant Fusion Proteins/biosynthesis , Small Ubiquitin-Related Modifier Proteins/metabolism , Staphylococcal Infections/enzymology , Staphylococcal Infections/genetics , Staphylococcal Infections/microbiology
3.
Acta Crystallogr Sect F Struct Biol Cryst Commun ; 68(Pt 11): 1341-5, 2012 Nov 01.
Article in English | MEDLINE | ID: mdl-23143245

ABSTRACT

CAD is a 243 kDa eukaryotic multifunctional polypeptide that catalyzes the first three reactions of de novo pyrimidine biosynthesis: glutamine-dependent carbamyl phosphate synthetase, aspartate transcarbamylase and dihydroorotase (DHO). In prokaryotes, these activities are associated with monofunctional proteins, for which crystal structures are available. However, there is no detailed structural information on the full-length CAD protein or any of its functional domains apart from that it associates to form a homohexamer of ∼1.5 MDa. Here, the expression, purification and crystallization of the DHO domain of human CAD are reported. The DHO domain forms homodimers in solution. Crystallization experiments yielded small crystals that were suitable for X-ray diffraction studies. A diffraction data set was collected to 1.75 Šresolution using synchrotron radiation at the SLS, Villigen, Switzerland. The crystals belonged to the orthorhombic space group C222(1), with unit-cell parameters a=82.1, b=159.3, c=61.5 Å. The Matthews coefficient calculation suggested the presence of one protein molecule per asymmetric unit, with a solvent content of 48%.


Subject(s)
Aspartate Carbamoyltransferase/chemistry , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/chemistry , Dihydroorotase/chemistry , Aspartate Carbamoyltransferase/biosynthesis , Aspartate Carbamoyltransferase/isolation & purification , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/biosynthesis , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/isolation & purification , Catalytic Domain , Chromatography, Affinity , Chromatography, Gel , Crystallization , Crystallography, X-Ray , Dihydroorotase/biosynthesis , Dihydroorotase/isolation & purification , Escherichia coli , Humans , Light , Protein Structure, Quaternary , Scattering, Radiation
4.
Biochemistry ; 48(4): 766-78, 2009 Feb 03.
Article in English | MEDLINE | ID: mdl-19128030

ABSTRACT

In prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (CPS), aspartate transcarbamoylase (ATC), and dihydroorotase (DHO), are commonly expressed separately and either function independently (Escherichia coli) or associate into multifunctional complexes (Aquifex aeolicus). In mammals the enzymes are expressed as a single polypeptide chain (CAD) in the order CPS-DHO-ATC and associate into a hexamer. This study presents the three-dimensional structure of the noncovalent hexamer of DHO and ATC from the hyperthermophile A. aeolicus at 2.3 A resolution. It is the first structure of any multienzyme complex in pyrimidine biosynthesis and is a possible model for the core of mammalian CAD. The structure has citrate, a near isosteric analogue of carbamoyl aspartate, bound to the active sites of both enzymes. Three active site loops that are intrinsically disordered in the free, inactive DHO are ordered in the complex. The reorganization also changes the peptide bond between Asp153, a ligand of the single zinc atom in DHO, and Gly154, to the rare cis conformation. In the crystal structure, six DHO and six ATC chains form a hollow dodecamer, in which the 12 active sites face an internal reaction chamber that is approximately 60 A in diameter and connected to the cytosol by narrow tunnels. The entrances and the interior of the chamber are both electropositive, which suggests that the architecture of this nanoreactor modifies the kinetics of the bisynthase, not only by steric channeling but also by preferential escape of the product, dihydroorotase, which is less negatively charged than its precursors, carbamoyl phosphate, aspartate, or carbamoyl aspartate.


Subject(s)
Aspartate Carbamoyltransferase/metabolism , Bacteria/enzymology , Dihydroorotase/metabolism , Multienzyme Complexes/metabolism , Pyrimidines/biosynthesis , Allosteric Regulation , Aspartate Carbamoyltransferase/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Binding Sites/physiology , Crystallography, X-Ray , Dihydroorotase/chemistry , Dihydroorotase/isolation & purification , Multienzyme Complexes/chemistry , Orotic Acid/analogs & derivatives , Orotic Acid/chemistry , Orotic Acid/metabolism , Protein Structure, Tertiary/physiology , Pyrimidines/chemistry , Static Electricity , Thermodynamics
6.
Arch Microbiol ; 164(5): 353-7, 1995 Nov.
Article in English | MEDLINE | ID: mdl-8572888

ABSTRACT

Dihydroorotase was purified to homogeneity from Pseudomonas putida. The relative molecular mass of the native enzyme was 82 kDa and the enzyme consisted of two identical subunits with a relative molecular mass of 41 kDa. The enzyme only hydrolyzed dihydro-L-orotate and its methyl ester, and the reactions were reversible. The apparent Km and Vmax values for dihydro-L-orotate hydrolysis (at pH 7.4) were 0.081 mM and 18 mumol min-1 mg-1, respectively; and those for N-carbamoyl-DL-aspartate (at pH 6.0) were 2.2 mM and 68 mumol min-1 mg-1, respectively. The enzyme was inhibited by metal ion chelators and activated by Zn2+. However, excessive Zn2+ was inhibitory. The enzyme was inhibited by sulfhydryl reagents, and competitively inhibited by N-carbamoylamino acids such as N-carbamoylglycine, with a Ki value of 2.7 mM. The enzyme was also inhibited non-competitively by pyrimidine-metabolism intermediates such as dihydrouracil and orotate, with a Ki value of 3.4 and 0.75 mM, respectively, suggesting that the enzyme activity is regulated by pyrimidine-metabolism intermediates and that dihydroorotase plays a role in the control of pyrimidine biosynthesis.


Subject(s)
Dihydroorotase/isolation & purification , Dihydroorotase/metabolism , Pseudomonas putida/enzymology , Chelating Agents/pharmacology , Chlorides/pharmacology , Dihydroorotase/antagonists & inhibitors , Dihydroorotase/chemistry , Enzyme Inhibitors/pharmacology , Hydrogen-Ion Concentration , Kinetics , Molecular Weight , Protein Conformation , Pyrimidines/metabolism , Substrate Specificity , Temperature
7.
Biochemistry ; 33(17): 5268-74, 1994 May 03.
Article in English | MEDLINE | ID: mdl-7909690

ABSTRACT

The malarial parasite Plasmodium falciparum can only synthesize pyrimidine nucleotides via the de novo pathway which is therefore a suitable target for development of antimalarial drugs. New assay procedures have been developed using high-pressure liquid chromatography (HPLC) which enable concurrent measurement of pyrimidine intermediates in malaria. Synchronized parasites growing in erythrocytes were pulse-labeled with [14C]bicarbonate at 6-h intervals around the 48-h asexual life cycle. Analysis of malarial extracts by HPLC showed tht incorporation of [14C]bicarbonate into pyrimidine nucleotides was maximal during the transition from trophozoites to schizonts. The reaction, N-carbamyl-L-aspartate-->L-dihydroorotate (CA-asp-->DHO) catalyzed by malarial dihydroorotase is inhibited by L-6-thiodihydroorotate (TDHO) in vitro (Ki = 6.5 microM), and TDHO, as the free acid or methyl ester, induces a major accumulation of CA-asp in malaria. Atovaquone, a naphthoquinone, is a moderate inhibitor of dihydroorotate dehydrogenase in vitro (Ki = 27 microM) but induces major accumulations of CA-asp and DHO. Pyrazofurin induces accumulation of orotate and orotidine in malaria, consistent with inhibition of orotidine 5'-monophosphate (OMP) decarboxylase with subsequent dephosphorylation of the OMP accumulated. Although TDHO, atovaquone, and pyrazofurin arrest the growth of P. falciparum, only moderate decreases in UTP, CTP, and dTTP were observed. 5-Fluoroorotate also arrests the growth of P. falciparum with major accumulations of 5-fluorouridine mono-, di-, and triphosphates and the most significant inhibition of de novo biosynthesis of pyrimidine nucleotides.


Subject(s)
Antimalarials/pharmacology , Dihydroorotase/metabolism , Naphthoquinones/pharmacology , Orotic Acid/analogs & derivatives , Orotidine-5'-Phosphate Decarboxylase/antagonists & inhibitors , Oxidoreductases Acting on CH-CH Group Donors , Plasmodium falciparum/metabolism , Pyrimidines/metabolism , Amides , Animals , Atovaquone , Bicarbonates/metabolism , Carbon Radioisotopes , Chromatography, High Pressure Liquid , Dihydroorotase/antagonists & inhibitors , Dihydroorotase/isolation & purification , Dihydroorotate Dehydrogenase , Erythrocytes/parasitology , Humans , Kinetics , Malaria/blood , Naphthoquinones/toxicity , Orotic Acid/pharmacology , Orotic Acid/toxicity , Oxidoreductases/isolation & purification , Oxidoreductases/metabolism , Plasmodium falciparum/drug effects , Plasmodium falciparum/growth & development , Pyrazoles , Pyrimidines/biosynthesis , Pyrimidines/isolation & purification , Ribonucleosides/pharmacology , Ribose
9.
Biochem Pharmacol ; 43(6): 1295-301, 1992 Mar 17.
Article in English | MEDLINE | ID: mdl-1348618

ABSTRACT

Dihydroorotase and dihydroorotate dehydrogenase, two enzymes of the pyrimidine biosynthetic pathway, were purified from Plasmodium berghei to apparent homogeneity. Orotate and a series of 5-substituted derivatives were found to inhibit competitively the purified enzymes from the malaria parasite. The order of effectiveness as inhibitors on pyrimidine ring cleavage reaction for dihydroorotase was 5-fluoro orotate greater than 5-amino orotate, 5-methyl orotate greater than orotate greater than 5-bromo orotate greater than 5-iodo orotate with Ki values of 65, 142, 166, 860, 2200 and greater than 3500 microM, respectively. 5-Fluoro orotate and orotate were the most effective inhibitors for dihydroorotate dehydrogenase. In vitro, 5-fluoro orotate and 5-amino orotate caused 50% inhibition of the growth of P. falciparum at concentrations of 10 nM and 1 microM, respectively. In mice infected with P. berghei, these two orotate analogs at a dose of 25 mg/kg body weight eliminated parasitemia after a 4-day treatment, an effect comparable to that of the same dose of chloroquine. The infected mice treated with 5-fluoro orotate at a lower dose of 2.5 mg/kg had a 95% reduction in parasitemia. The effects of the more potent compounds tested in combination with inhibitors of other enzymes of this pathway on P. falciparum in vitro and P. berghei in vivo are currently under investigation. These results suggest that the pyrimidine biosynthetic pathway in the malarial parasite may be a target for the design of antimalarial drugs.


Subject(s)
Antimalarials/pharmacology , Dihydroorotase/antagonists & inhibitors , Orotic Acid/analogs & derivatives , Oxidoreductases Acting on CH-CH Group Donors , Oxidoreductases/antagonists & inhibitors , Plasmodium berghei/drug effects , Plasmodium falciparum/drug effects , Animals , Antimalarials/therapeutic use , Chloroquine/pharmacology , Dihydroorotase/isolation & purification , Dihydroorotate Dehydrogenase , Kinetics , Macrophages/drug effects , Malaria/drug therapy , Mice , Orotic Acid/pharmacology , Oxidoreductases/isolation & purification , Plasmodium berghei/enzymology , Pyrimidines/biosynthesis
10.
Protein Expr Purif ; 1(1): 45-8, 1990 Sep.
Article in English | MEDLINE | ID: mdl-1983795

ABSTRACT

Dihydroorotate (DHO) synthetase is a trifunctional protein that catalyzes the first three reactions of de novo pyrimidine biosynthesis. A single-step procedure for purification of DHO synthetase from mutant hamster cells that overproduce this protein has been developed. The synthetase is adsorbed from a postmitochondrial supernatant to a column of Procion blue-Sepharose 4B and, after the column is washed, the synthetase is eluted as a single peak with 0.4 M KCl. Pooled fractions from the trailing side of this peak yield DHO synthetase with a specific activity for aspartate transcarbamylase of 14 mumol/min/mg protein, representing a purification factor of 8.5-fold and a recovery of 28% from the postmitochondrial supernatant. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that the DHO synthetase was of high purity. A further 34% of the DHO synthetase from the leading side of the eluted peak contained a minor proportion of a proteolytic fragment. Similar results were obtained with an established four-step purification procedure.


Subject(s)
Aspartate Carbamoyltransferase/isolation & purification , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/isolation & purification , Chromatography, Agarose/methods , Dihydroorotase/isolation & purification , Multienzyme Complexes/isolation & purification , Animals , Aspartate Carbamoyltransferase/chemistry , Aspartate Carbamoyltransferase/genetics , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/chemistry , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/genetics , Cell Line , Coloring Agents , Cricetinae , Dihydroorotase/chemistry , Dihydroorotase/genetics , Multienzyme Complexes/chemistry , Multienzyme Complexes/genetics , Mutation , Triazines
11.
Biochemistry ; 29(26): 6270-5, 1990 Jul 03.
Article in English | MEDLINE | ID: mdl-1976382

ABSTRACT

Dihydroorotase (DHOase) catalyzes the reversible cyclization of N-carbamoyl-L-aspartate (L-CA) to L-5,6-dihydroorotate (L-DHO), which is the third enzyme in de novo pyrimidine biosynthesis. The enzyme was purified from two parasitic protozoa, Crithidia fasciculata (about 16,000-fold) and Plasmodium berghei (about 790-fold). The C. fasciculata enzyme had a native molecular weight (Mr) of 42,000 +/- 5000, determined by gel filtration chromatography, and showed a single detectable protein band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with Mr 44,000 +/- 3000. The DHOase from P. berghei had a native molecular weight of 40,000 +/- 4000 and a subunit molecular weight on SDS-PAGE of 38,000 +/- 3000. The DHOase from both parasites, in contrast to the mammalian enzyme which resides on a trifunctional protein of the first two enzymes of the pathway, carbamoyl-phosphate synthase and aspartate transcarbamylase, is monomeric and has no oligomeric structure as studied by chemical cross-linking with dimethyl suberimidate. The rate of cyclization of L-CA by the C. fasciculata enzyme was relatively high at acidic pH, decreasing to a very low rate at alkaline pH. In contrast, the rate of ring cleavage of L-DHO was very low at acidic pH and increased to a higher rate at alkaline pH. These pH-activity profiles gave an intersection at pH 6.6. The Km and kcat for L-CA were 0.846 +/- 0.017 mM and 39.2 +/- 6.4 min-1, respectively; for L-DHO, they were 25.85 +/- 2.67 microM and 258.6 +/- 28.5 min-1.(ABSTRACT TRUNCATED AT 250 WORDS)


Subject(s)
Crithidia/enzymology , Dihydroorotase/isolation & purification , Plasmodium berghei/enzymology , Pyrimidines/biosynthesis , Animals , Aspartic Acid/analogs & derivatives , Aspartic Acid/metabolism , Chromatography, Gel , Dihydroorotase/metabolism , Dimethyl Sulfoxide/pharmacology , Kinetics , Molecular Weight , Orotic Acid/analogs & derivatives , Orotic Acid/metabolism
12.
Biochemistry ; 28(2): 463-70, 1989 Jan 24.
Article in English | MEDLINE | ID: mdl-2565732

ABSTRACT

In mammals, dihydroorotase is part of a trifunctional protein, dihydroorotate synthetase, which catalyzes the first three reactions of de novo pyrimidine biosynthesis. Dihydroorotase catalyzes the formation of a peptide-like bond between the terminal ureido nitrogen and the beta-carboxyl group of N-carbamyl-L-aspartate to yield heterocyclic L-dihydroorotate. A variety of evidence suggests that dihydroorotase may have a catalytic mechanism similar to that of a zinc protease [Christopherson, R. I., & Jones, M. E. (1980) J. Biol. Chem. 255, 3358-3370]. Tight-binding inhibitors of the zinc proteases, carboxypeptidase A, thermolysin, and angiotensin-converting enzyme have been synthesized that combine structural features of the substrates with a thiol or carboxyl group in an appropriate position to coordinate a zinc atom bound at the catalytic site. We have synthesized (4R)-2-oxo-6-thioxohexahydropyrimidine-4-carboxylate (L-6-thiodihydroorotate) and have found that this analogue is a potent competitive inhibitor of dihydroorotase with a dissociation constant (Ki) in the presence of excess Zn2+ ion of 0.17 +/- 0.02 microM at pH 7.4. The potency of inhibition by L-6-thiodihydroorotate in the presence of divalent metal ions decreases in the order Zn2+ greater than Ca2+ greater than Co2+ greater than Mn2+ greater than Ni2+; L-6-thiodihydroorotate alone is less inhibitory and has a Ki of 0.85 +/- 0.14 microM. 6-Thioorotate has a Ki of 82 +/- 8 microM which decreases to 3.8 +/- 1.4 microM in the presence of Zn2+. Zn2+ alone is a moderate inhibitor of dihydroorotase and does not enhance the potency of other inhibitors.(ABSTRACT TRUNCATED AT 250 WORDS)


Subject(s)
Amidohydrolases/antagonists & inhibitors , Dicarboxylic Acids/chemical synthesis , Dihydroorotase/antagonists & inhibitors , Pyrimidines/chemical synthesis , Sulfhydryl Compounds/pharmacology , Animals , Binding, Competitive , Cations, Divalent , Cell Line , Cricetinae , Cysteine/analogs & derivatives , Cysteine/pharmacology , Dicarboxylic Acids/pharmacology , Dihydroorotase/isolation & purification , Indicators and Reagents , Kinetics , Magnetic Resonance Spectroscopy , Pyrimidines/pharmacology , Structure-Activity Relationship , Substrate Specificity
13.
J Biol Chem ; 263(2): 708-13, 1988 Jan 15.
Article in English | MEDLINE | ID: mdl-2891701

ABSTRACT

Leishmania donovani is a protozoal pathogen that belongs to the kinetoplastida order. Unlike in other eucaryotic systems, the first three enzymes of the de novo pyrimidine biosynthetic pathway are not components of a multifunctional protein system. The three enzyme activities in the crude extract were separated on a Sephacryl S-200 column. Aspartate carbamoyltransferase (EC 2.1.3.2) has been purified to apparent homogeneity. The enzyme has an approximate molecular weight of 135,000 and seems to be a tetramer of equivalent subunits of molecular weight 35,000. The enzyme shows strictly hyperbolic kinetics with both the substrates under a variety of conditions and is not inhibited by nucleotide phosphates. Km for carbamyl phosphate is 3.1 x 10(-4) M and for aspartate is 7.6 x 10(-3) M. Apparently, the enzyme has no regulatory role in pyrimidine biosynthesis. N-(Phosphonoacetyl)-L-aspartic acid is a powerful competitive inhibitor (Ki = 5 x 10(-7) M) for this enzyme with carbamyl phosphate as substrate. This inhibitor completely inhibits the growth of the vector form of organism at 60 microM and significantly affects the growth of the pathogenic form in a macrophage assay system. The potency of the inhibitor is comparable with allopurinol which is undergoing human clinical trial as an antileishmanial drug.


Subject(s)
Aspartate Carbamoyltransferase/antagonists & inhibitors , Aspartic Acid/analogs & derivatives , Leishmania donovani/enzymology , Organophosphorus Compounds/pharmacology , Phosphonoacetic Acid/pharmacology , Animals , Aspartic Acid/pharmacology , Aspartic Acid/therapeutic use , Carbamoyl-Phosphate Synthase (Ammonia)/isolation & purification , Chromatography, Gel , Cricetinae , Dihydroorotase/isolation & purification , Leishmaniasis/drug therapy , Pentamidine/pharmacology , Phosphonoacetic Acid/analogs & derivatives , Phosphonoacetic Acid/therapeutic use
14.
J Biol Chem ; 261(27): 12477-85, 1986 Sep 25.
Article in English | MEDLINE | ID: mdl-2875071

ABSTRACT

We have systematically characterized, by aqueous column chromatography on a size exclusion cross-linked dextran gel (Sephadex G-10), 12 solutes, 11 of which are known to affect protein stability. Six are chaotropes (water structure breakers) and destabilize proteins, while five are polar kosmotropes (polar water structure makers) and stabilize proteins. Analysis of the chromatographic behavior of these neutral (ethylene glycol, urea), positively charged (Tris, guanidine, as the hydrochloride salts) and negatively charged (SO2-4, HPO2-4, F-, Cl-, Br-, Cl3CCO-2, I-, SCN-, as the sodium salts, in order of elution) solutes at pH 7 as a function of sample concentration (up to 0.6 M), supporting electrolyte, and temperature yields four conclusions, based largely on the behavior of the anions. Chaotropes adsorb to the gel according to their position in the Hofmeister series, with the most chaotropic species adsorbing most strongly. ++Chaotropes adsorb to the gel less strongly in the presence of chaotropes (a salting in effect) and more strongly in the presence of polar kosmotropes (a salting out effect). Polar kosmotropes do not adsorb to the gel, and are sieved through the gel according to their position in the Hofmeister series, with the most kosmotropic species having the largest relative hydrodynamic radii. The hydrodynamic radii of polar kosmotropes is increased by chaotropes and decreased by polar kosmotropes. These results suggest that a chaotrope interacts with the first layer of immediately adjacent water molecules somewhat less strongly than would bulk water in its place; a polar kosmotrope, more strongly.


Subject(s)
Amidohydrolases/isolation & purification , Dihydroorotase/isolation & purification , Solutions , Water , Anions , Cations , Chemical Phenomena , Chemistry, Physical , Chromatography, Gel/methods , Dihydroorotase/metabolism , Electrolytes , Escherichia coli/enzymology , Kinetics , Temperature
15.
J Biol Chem ; 261(13): 5920-9, 1986 May 05.
Article in English | MEDLINE | ID: mdl-2871020

ABSTRACT

We have obtained 53 mg of 99% pure dihydroorotase from 10.9 g of frozen Escherichia coli pyrC plasmid-containing E. coli cells using a 4-step 16-fold purification procedure, a yield of 60%. We characterize the enzyme by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (a dimer of subunit molecular weight 38,300 +/- 2,900), high performance liquid chromatography gel sieving, amino acid analysis, amino terminus determination (blocked), and specific activity. The isolated enzyme contains 1 tightly bound essential zinc atom/subunit, and readily but loosely binds 2 additional Zn(II) or Co(II) ions/subunit which modulate catalytic activity; treatment of crude extracts with weak chelators suggests that the enzyme contains 3 zinc atoms/subunit in vivo. Two of the 6 thiol groups/subunit react rapidly with 5,5'-dithiobis(2-nitrobenzoate) when 1 Zn/subunit enzyme is used, but slowly when 3 Zn/subunit enzyme is used. The 2 weakly bound Zn(II) ions/subunit protect against the reversible air oxidation which lowers the specific activity of the enzyme and renders it unreactive with 5,5'-dithiobis(2-nitrobenzoate). The dilution activation observed in the presence of substrate, the dilution inactivation observed in the absence of substrate, and the transient activation by the metal chelator oxalate are interpreted as evidence for an unstable, hyperactive monomer.


Subject(s)
Amidohydrolases/metabolism , Cobalt/analysis , Dihydroorotase/metabolism , Escherichia coli/enzymology , Zinc/analysis , Amino Acids/analysis , Binding Sites , Dihydroorotase/genetics , Dihydroorotase/isolation & purification , Dithionitrobenzoic Acid/pharmacology , Escherichia coli/genetics , Kinetics , Macromolecular Substances , Molecular Weight , Plasmids , Protein Binding , Sulfhydryl Compounds/analysis
16.
J Biol Chem ; 261(13): 6073-83, 1986 May 05.
Article in English | MEDLINE | ID: mdl-2871022

ABSTRACT

Dihydroorotase (DHOase) catalyzes the third step in eukaryotic de novo pyrimidine biosynthesis. In mammalian cells, this enzyme activity is carried by a large chimeric protein, CAD, that also catalyzes the first two steps in the pathway: glutamine-dependent carbamyl phosphate synthetase (CPSase) and aspartate transcarbamylase (ATCase). Controlled elastase cleavage of CAD released a 44,000 +/- 2,000-dalton proteolytic fragment which catalyzed only the dihydroorotase reaction. We have devised a rapid and simple method for the isolation of the DHO domain from elastase digests. The domain, which was obtained in 36% yield, was found to be homogeneous by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and isoelectric focusing. The domain was also characterized by amino acid analysis and analytical high pressure liquid chromatography peptide mapping. The amino terminus of both the DHO domain and intact CAD was blocked suggesting that this domain is located at the extreme amino terminus of the CAD polypeptide, a result consistent with the suspected juxtaposition of domains as DHO-CPS-ATC. The isoelectric point of the DHO domain was 5.1, while that of the ATC domain was 9.4, so that the ends of the CAD polypeptide are oppositely charged at physiological pH. Immunoblotting with DHO domain-specific antibodies showed that a 47-kDa species was generated in the early stages of controlled proteolysis of CAD. Thus there are two elastase cleavage sites within a 3-kDa connecting region that links the DHO and CPS domains. The domain was shown by atomic absorption spectrophotometry and by isolating a 65Zn-containing DHO domain from mammalian cells grown in the presence of the radionuclide to contain 1 g eq of tightly bound zinc in each polypeptide chain. Zinc was not found in any other CAD domain. Chelating agents inhibit dihydroorotase activity of the isolated domain supporting the conclusion, based on studies of intact CAD by others, that zinc participates in catalysis. At moderate protein concentrations the DHO domain was a 88,000 dimer with a Stokes radius of 37.6 A, a S20,w = 5.1 X 10(-13) s, a diffusion coefficient of 3.17 X 10(-7) cm2 s-1, and a frictional ratio of 1.26. On dilution the dimer dissociated and was in rapid concentration-dependent equilibrium with a 43,500 monomer. The hydrodynamic parameters of the monomer have also been estimated (Stokes radius of 29.8 A, D20,w = 4.11 X 10(-7) cm2 s-1, and f/f0 1.21).(ABSTRACT TRUNCATED AT 400 WORDS)


Subject(s)
Amidohydrolases/metabolism , Aspartate Carbamoyltransferase , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) , Dihydroorotase/metabolism , Multienzyme Complexes , Proteins/metabolism , Zinc/analysis , Amino Acids/analysis , Animals , Cell Line , Cell Transformation, Viral , Cricetinae , Dihydroorotase/isolation & purification , Kinetics , Macromolecular Substances , Mesocricetus , Molecular Weight , Peptide Fragments/analysis , Simian virus 40/genetics
17.
Biochem J ; 230(1): 101-8, 1985 Aug 15.
Article in English | MEDLINE | ID: mdl-2864918

ABSTRACT

A new purification procedure involving five column-chromatography steps is described for dihydro-orotase (L-5,6-dihydro-orotate amidohydrolase, EC 3.5.2.3) from Clostridium oroticum (A.T.C.C. 25750). The native purified enzyme is a dimer of Mr 102 000 and contains 4.0 +/- 0.3 g-atoms of zinc/mol of dimer. These observations agree with those reported previously [Taylor, Taylor, Balch & Gilchrist (1976) J. Bacteriol. 127, 863-873]. It is conclusively demonstrated that dihydro-orotase is a zinc metalloenzyme. Zinc is reversibly removed by treatment with chelators in phosphate buffer at pH 6.5, as demonstrated by atomic absorption spectrophotometry and decrease of enzyme activity. The specific activity is linearly dependent on zinc content. Addition of ZnSO4 to the chelator-treated enzyme results in regain of the normal complement of zinc and enzyme activity. Kinetic properties of the reconstituted enzyme are indistinguishable from those of the native enzyme. The amino acid composition of the homogeneous enzyme suggests that the zinc atoms occupy different environments.


Subject(s)
Amidohydrolases/metabolism , Clostridium/enzymology , Dihydroorotase/metabolism , Zinc/analysis , Amino Acids/analysis , Chromatography, Liquid , Dihydroorotase/antagonists & inhibitors , Dihydroorotase/isolation & purification , Edetic Acid/pharmacology , Electrophoresis, Polyacrylamide Gel , Kinetics
18.
J Biol Chem ; 259(5): 3293-8, 1984 Mar 10.
Article in English | MEDLINE | ID: mdl-6142052

ABSTRACT

Dihydroorotase (4,5-L-dihydroorotate amidohydrolase (EC 3.5.2.3], which catalyzes the reversible cyclization of N-carbamyl-L-aspartate to dihydro-L-orotate, has been purified to homogeneity from an over-producing strain of Escherichia coli. Treatment of 70 g of frozen cell paste produces about 7 mg of pure enzyme, a yield of about 35%. The native molecular weight, determined by equilibrium sedimentation, is 80,900 +/- 4,300. The subunit molecular weight, determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis is 38,400 +/- 2,600, and by amino acid analysis is 41,000. The enzyme is thus a dimer and contains 0.95 +/- 0.08 tightly bound zinc atoms per subunit when isolated by the described procedure, which would remove any loosely bound metal ions. Isoelectric focusing under native conditions yields a major species at isoelectric point 4.97 +/- 0.27 and a minor species at 5.26 +/- 0.27; dihydroorotase activity is proportionately associated with both bands. The enzyme has a partial specific volume of 0.737 ml/g calculated from the amino acid composition and a specific absorption at 278 nm of 0.638 for a 1 mg/ml solution. At 30 degrees C, the Michaelis constant and kcat for dihydro-DL-orotate (at pH 8.0) are 0.0756 mM and 127 s-1, respectively; for N-carbamyl-DL-aspartate (at pH 5.80), they are 1.07 mM and 195 s-1.


Subject(s)
Amidohydrolases/isolation & purification , Dihydroorotase/isolation & purification , Escherichia coli/enzymology , Amino Acids/analysis , Dihydroorotase/metabolism , Kinetics , Macromolecular Substances , Molecular Weight , Spectrophotometry, Atomic , Spectrophotometry, Ultraviolet , Zinc/analysis
20.
Mol Biochem Parasitol ; 1(1): 55-68, 1980 Mar.
Article in English | MEDLINE | ID: mdl-6108508

ABSTRACT

Glutamine-dependent carbamoyl-phosphate synthetase, the first enzyme of the de novo biosynthetic pathway for pyrimidine nucleotides, was purified about twenty-fold from 105 000 x g supernatant of the Ascaris ovary homogenate. The enzyme activity was feedback-inhibited by UDP and UTP while it was stimulated by 5-phosphoribosyl 1-pyrophosphate. Most of the catalytic and regulatory properties of the Ascaris synthetase were similar to those of the mammalian synthetase. A significant difference is that the Ascaris enzyme was more strongly inhibited by UDP than by UTP whereas the mammalian enzyme is more sensitive to UTP than to UDP. The Ascaris enzyme was also inhibited by other various nucleoside diphosphates, such as dUDP, dADP and CDP, generally more strongly than by the corresponding nucleoside triphosphates. Aspartate carbamoyltransferase and dihydroorotase, the second and third enzymes of the pathway, were also demonstrated in the supernatant fraction. These two enzymes were copurified with the synthetase and the relative activities of the three enzymes remained nearly constant (1:850-890:50-60) throughout the purification. In a sucrose gradient centrifugation, the enzymes cosedimented as a single peak with a sedimentation coefficient (s20,w) of about 32 S under the condition used. These results strongly suggest that the enzymes exist as a multienzyme complex similar to those found in higher animals. The activity of the carbamoyltransferase was insensitive to nucleotides and related compounds. These results indicate that the synthetase plays a key role in the control of pyrimidine biosynthesis in the Ascaris ovary.


Subject(s)
Amidohydrolases/metabolism , Ascaris/enzymology , Aspartate Carbamoyltransferase/metabolism , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/metabolism , Dihydroorotase/metabolism , Ligases/metabolism , Pyrimidines/biosynthesis , Animals , Aspartate Carbamoyltransferase/isolation & purification , Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/isolation & purification , Dihydroorotase/isolation & purification , Female , Ovary/enzymology
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