Allantoin degradation by Saccharomyces cerevisiae--a model system for gene regulation and metabolic integration.
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Allantoin↗
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Crystal structure of ureidoglycolate hydrolase (AllA) from Escherichia coli O157:H7.
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Amidine-Lyases↗
The ureidoglycollate hydrolase (DAL3) gene in Saccharomyces cerevisiae.
The DAL3 gene has been sequenced and found to encode a 195 amino acid protein with a molecular weight of 21,727. The four carboxy-terminal amino acids of DAL3 product (Cys-Ile-Ile-Ile) are homologous to those (CAAX) previously shown to be the primary structural signal for post-translational farnesylation of yeast RAS protein and mating factor. This modification is reported to be responsible for membrane localization of proteins containing it. The upstream region of DAL3 contains six copies of a sequence that is homologous to the positively acting DAL UASNTR reported to be required for transcriptional activation of the DAL5 and DAL7 genes. Missing from the DAL3 upstream region were any sequences related to those shown to be required for a DAL7 response to inducer, the UIS element. This correlates with the previous report that DAL3 expression is independent of the allantoin pathway inducer.
Amidine-Lyases↗
A continuous spectrophotometric assay for ureidoglycolase activity with lactate dehydrogenase or glyoxylate reductase as coupling enzyme.
A spectrophotometric assay for ureidoglycolase activity (both ureidoglycolate lyase and hydrolase), based on the reduction of glyoxylate to glycolate catalyzed by glyoxylate reductase or lactate dehydrogenase with the stoichiometric and continuous NADH oxidation, is described. The assay has been optimized for the amount of coupling enzyme, reagent concentrations, buffers, and the nonenzymatic degradation of ureidoglycolate. Under optimal assay conditions, ureidoglycolase activity can be followed with either lactate dehydrogenase or glyoxylate reductase as coupling enzyme and reaction can be started by addition of substrate or enzyme extract. Once the reaction was started, NADH oxidation was linear with time after a lag phase of 1-2 min. This linear NADH oxidation was directly proportional to enzyme concentration in the assay mixture until changes in absorbance of 0.12 per minute. This method is easy and reliable for the accurate determination of ureidoglycolase activity in crude and purified extracts from Chlamydomonas reinhardtii cells and no notable interferences have been detected. Since lactate dehydrogenase is much cheaper and has a lower Km for its substrate than glyoxylate reductase and can be used as supplied, its use as the coupling enzyme of choice is recommended.
Alcohol Oxidoreductases↗
Catabolite repression and nitrogen control of allantoin-degrading enzymes in Pseudomonas aeruginosa.
The formation of the allantoin-degrading enzymes allantoinase, allantoicase and ureidoglycolase in Pseudomonas aeruginosa was found to be regulated by induction, catabolite repression and nitrogen control. Induction was observed when urate, allantoin or allantoate were included in the growth medium, but not with ureidoglycolate. Tricarboxylic acid cycle intermediates exerted catabolite repression of the synthesis of the three enzymes, while pyruvate and glucose caused less repression. The operation of a nitrogen control mechanism in the regulation of the allantoin-degrading enzymes could be demonstrated with glutamine synthetase-negative mutants, which showed elevated synthesis and escape from catabolite repression when growth was limited for glutamine.
Allantoin↗
Metabolism of allantoin in Hyphomicrobium species.
Hyphomicrobium species are able to use allantoin as a nitrogen source for growth. Allantoin is broken down to glyoxylate and ammonia by the consecutive action of allantoinase, allantoicase, ureidoglycolase and urease.
Allantoin↗
Purine degradation in the edible mushroom Agaricus bisporus.
Agaricus bisporus is able to use urate, allantoin, allantoate, urea and alloxanate as nitrogen sources for growth. The presence of urate oxidase, allantoinase, ureidoglycolase and urease activities, both in fruit bodies and mycelia, points to a degradative pathway for urate similar to that found in various microorganisms. So far all efforts to demonstrate the enzyme responsible for allantoate degradation failed. A urease inhibitor appeared to be present in cell-free extracts from fruit bodies.
Agaricus↗
New insights into copper monooxygenases and peptide amidation: structure, mechanism and function.
Many bioactive peptides must be amidated at their carboxy terminus to exhibit full activity. Surprisingly, the amides are not generated by a transamidation reaction. Instead, the hormones are synthesized from glycine-extended intermediates that are transformed into active amidated hormones by oxidative cleavage of the glycine N-C alpha bond. In higher organisms, this reaction is catalyzed by a single bifunctional enzyme, peptidylglycine alpha-amidating monooxygenase (PAM). The PAM gene encodes one polypeptide with two enzymes that catalyze the two sequential reactions required for amidation. Peptidylglycine alpha-hydroxylating monooxygenase (PHM; EC 1.14.17.3) catalyzes the stereospecific hydroxylation of the glycine alpha-carbon of all the peptidylglycine substrates. The second enzyme, peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL; EC 4.3.2.5), generates alpha-amidated peptide product and glyoxylate. PHM contains two redox-active copper atoms that, after reduction by ascorbate, catalyze the reduction of molecular oxygen for the hydroxylation of glycine-extended substrates. The structure of the catalytic core of rat PHM at atomic resolution provides a framework for understanding the broad substrate specificity of PHM, identifying residues critical for PHM activity, and proposing mechanisms for the chemical and electron-transfer steps in catalysis. Since PHM is homologous in sequence and mechanism to dopamine beta-monooxygenase (DBM; EC 1.14.17.1), the enzyme that converts dopamine to norepinephrine during catecholamine biosynthesis, these structural and mechanistic insights are extended to DBM.
Amidine-Lyases↗
Two SINE families associated with equine microsatellite loci.
BLAST searches of 61 equine microsatellite sequences revealed two related families of retroposons. The first family included seven markers, all of which showed significant homology to the Equine Repetitive Element-1 (ERE-1) Short Interspersed Nucleotide Element (SINE) sequence. Length of homology ranged from 76 to 171 bases with identities to the ERE-1 consensus sequence ranging from 71% to 83%. The second family referred to as Equine Repetitive Element-2 (ERE-2) has a consensus sequence that showed homology to ERE-1 over approximately 60 bases. These 60 bases comprised subunit I. Sequence comparisons for the two retroposons led to the identification of a subunit II, subunit III, as well as the tRNAser subunit. The subunit structure of ERE-1 was tRNAser-I-II. By contrast, the subunit structure of ERE-2 was I-III-III. The nine markers related to ERE-2 showed homology lengths ranging from 84 to 163 bases with identities ranging from 75% to 99%. In addition to being present in microsatellites, ERE-2 appeared in three separate equine genes. It occurred in an intron of DNA-PK, in an untranslated region as well as in the promoter of PGHS, and in the coding region of PAM. The amino acids corresponding to the ERE-2 sequence in PAM were not present in the human or mouse PAM homologs. These amino acids associated with the ERE-2 sequence were present on the cytosolic side of the transmembrane domain of the PAM enzyme. Microsatellite markers in the ERE-1 and ERE-2 families were found throughout the genus equus and also for rhinoceros, indicating that the appearance of both retroposons predates the divergence of equids from the other perissodactyls. The markers did not amplify in human or bovine DNA. This indicated that ERE-1 and ERE-2 are, at least, perissodactyl specific.
Amidine-Lyases↗
Degradation of ureidoglycolate in French bean (Phaseolus vulgaris) is catalysed by a ubiquitous ureidoglycolate urea-lyase.
A ureidoglycolate-degrading activity was analysed in different tissues of French bean (Phaseolus vulgaris L.) plants during development. Activity was detected in all the tissues analysed, although values were very low in seeds before germination and in cotyledons. After radicle emergence, the activity increased due to high activity present in the axes. The highest levels of specific activity were found in developing fruits, from which the enzyme was purified and characterised. This is the first ureidoglycolate-degrading activity that has been purified to homogeneity from a ureide legume. The enzyme was purified 280 fold, and the specific activity for the pure enzyme was 4.4 units mg(-1), which corresponds to a turnover number of 1,055 min(-1). The native enzyme has a molecular mass of 240 kDa and consists of six identical or similar-sized subunits each of 38 kDa. The activity of the purified enzyme was completely dependent on manganese and asparagine. The enzyme exhibited hyperbolic, Michaelian kinetics for ureidoglycolate with a K(m) value of 3.9 mM. This enzyme has been characterised as a ureidoglycolate urea-lyase (EC 4.3.2.3).
Amidine-Lyases↗
Ureidoglycolate amidohydrolase from developing French bean fruits (Phaseolus vulgaris [L.].).
Ureidoglycolate is an intermediate of allantoin catabolism in ureide-transporting legumes. This report describes the first purification of ureidoglycolate degrading activity (UGDA) from plant tissue in which the enzyme has been separated from urease. The enzyme from developing fruits of Phaseolus vulgaris has been purified 48-fold to give a preparation free of allantoinase and urease activity. UGDA was inhibited by EDTA while the Vmax was increased in the presence of Mn2+. The Km values for ureidoglycolate in the presence and the absence of Mn2+ were 2.0 and 5.4 mM, respectively. In the absence of Mn2+ UGDA was heat labile at 40 degrees C, but in the presence of Mn2+ the activity was stable up to temperatures of 60 degrees C. The Mr of UGDA was determined to be 300,000 by gel filtration chromatography and the pH optimum ranged from pH 7.0 to 8.5. Ammonia was determined to be the nitrogen-containing product of UGDA by a microdiffusion assay. This enzyme should therefore be described as ureidoglycolate amidohydrolase. The activity was shown to be associated with peroxisomes by fractionation of a crude extract on a sucrose density gradient. The products of ureidoglycolate degradation are glyoxylate, ammonia, and presumably carbon dioxide, which can be readily utilized by pathways of metabolism that are known to be present in this organelle.
Amidine-Lyases↗
The 108-kDA peptidylglycine alpha-amidating monooxygenase precursor contains two separable enzymatic activities involved in peptide amidation.
A 43-kDa protein factor that increases the ability of purified bovine peptidylglycine alpha-amidating monooxygenase (PAM)-A and -B to produce alpha-amidated peptides at physiological pH was purified to homogeneity from bovine neurointermediate pituitary. At each step of the purification, the amount of activity correlated with the amount of protein detected on Western blots by antibody to bovine PAM(561-579). In the bovine neurointermediate pituitary the 108-kDa PAM precursor protein is cleaved to form a peptidylglycine alpha-hydroxylating monooxygenase and a peptidyl-alpha-hydroxyglycine alpha-amidating lyase, which function sequentially in the 2-step formation of alpha-amidated peptides.
Amidine-Lyases↗
Peptide amidating enzymes are present in cultured endothelial cells.
Carboxy-terminal amidation is a prevalent post-translational modification necessary for the bioactivity of many peptides. We now report that the two enzymes essential for amidation, peptidylglycine alpha-monooxygenase (PAM) and peptidylamidoglycolate lyase (PGL), are present in both the cytosol and membrane fractions of cultured bovine aortic endothelial cells. Endothelial PAM exhibits ascorbate-dependent turnover and is inactivated by the mechanism-based inactivator, 4-phenyl-3-butenoic acid (PBA), whereas PGL activity is independent of ascorbate and is not affected by PBA. These enzymological characteristics correspond to those of amidating enzymes from other tissues. These results suggest a heretofore unrecognized role for alpha-amidated peptides in cardiovascular function.
Amidine-Lyases↗
Peptide amidation.
Many hormones, neurotransmitters and growth factors are peptides that carry an amide group at their carboxyl terminus which is essential for their biological activity. The amide is formed by hydroxylation of an additional glycine residue present in the biosynthetic precursor and the hydroxyglycine derivative dissociates to form the peptide amide and glyoxylic acid. Recent discoveries have shown that two enzymes are involved that act sequentially.
Amidine-Lyases↗
High-performance liquid chromatographic enantiomeric separation of an enzyme inhibitor which possesses both a chiral center and tautomeric moieties.
The enantiomeric separation using high-performance liquid chromatography (HPLC) on chiral stationary phases (CSPs) of a chiral compound which exists in solution in several tautomeric forms is described. 2,4-Dioxo-5-acetamido-6-phenylhexanoic acid is the most potent inhibitor known for peptidylamidoglycolate lyase (PGL, EC 4.3.2.5), an enzyme which plays an essential role in carboxyl-terminal amidation of many biological peptides. Synthesis of this inhibitor entails an alkaline hydrolysis step, under which condition the compound is racemized; thus, HPLC with a CSP was employed to obtain the individual enantiomers of this inhibitor. Since 2,4-dioxo-5-acetamido-6-phenylhexanoic acid exists in solution in several tautomeric forms, the strategy of first converting this compound from its multiple enol forms into a single diketo tautomer, which was then applied to various CSPs, was employed. Successful preparative scale enantiomeric separation of this compound was achieved using a Chiralpak AD CSP. Enantiomeric separation was also accomplished on a D-penicillamine column, but this CSP was found to be less satisfactory for preparative purposes.
Acetamides↗
Determination of the absolute configuration of alpha-hydroxyglycine derivatives by enzymatic conversion and chiral high-performance liquid chromatography.
We describe an approach for facile determination of the absolute configuration of enantiomerically chromatographed racemates by combining enzymatic conversion and chiral chromatography. The method involves initial rapid development of chiral HPLC methods using polar organic eluents with polysaccharide chiral phases. We present here evidence for using the stereospecific peptidylamidoglycolate lyase (PGL, E.C. 4.3.2.5) to determine the absolute configuration of alpha-hydroxyglycine derivatives. The racemic solute was incubated with PGL, lyophilized and then enantiomerically chromatographed using the CHIRALPAK AD column. Based on the specificity of the enzyme reaction, the unreacted enantiomer was assigned the absolute configuration R.
Amidine-Lyases↗
Expression and characterization of human bifunctional peptidylglycine alpha-amidating monooxygenase.
We report the purification and characterization of human bifunctional peptidylglycine alpha-amidating monooxygenase (the bifunctional PAM) expressed in Chinese hamster ovary cells. PAM is in charge of the formation of the C-terminal amides of biologically active peptides. The bifunctional PAM possesses two catalytic domains in a single polypeptide, peptidylglycine alpha-hydroxylating monooxygenase (PHM, EC 1.14.17.3) and peptidylamidoglycolate lyase (PAL, EC 4.3.2.5). By introducing a stop codon at 835 Glu, we were able to eliminate the membrane-spanning domain in the C-terminal region and succeeded in purifying a soluble form of bifunctional PAM that was secreted into the medium. Through a three-step purification procedure, we obtained 0.3mg of the purified PAM, which showed a single band at 91 kDa on SDS-PAGE, from 1L of monolayer culture medium. Metals contained in the purified PAM were analyzed and chemical modifications were performed to gain insight into the mechanism of the PAL reaction. Inductively coupled plasma detected 0.62 mol of Zn(2+) and 1.25 mol of Cu(2+) per mol of bifunctional PAM. Further, the addition of 1mM EDTA reduced the PAL activity by about 50%, but the decreased activity was recovered by the addition of an excess amount of Zn(2+). In a series of chemical modifications, phenylglyoxal almost completely eliminated the PAL activity and diethyl pyrocarbonate suppressed activity by more than 70%. These findings implied that Arg and His residues might play crucial roles during catalysis.
Amidine-Lyases↗
Functional and structural characterization of peptidylamidoglycolate lyase, the enzyme catalyzing the second step in peptide amidation.
Carboxy-terminal amidation is a prevalent posttranslational modification necessary for the bioactivity of many neurohormonal peptides. We recently reported that in addition to peptidylglycine alpha-monooxygenase (PAM), a second enzyme, which we now call peptidylamidoglycolate lyase (PGL), functions in the enzymatic formation of amides [Katopodis et al. (1990) Biochemistry 29, 4551]. The monooxygenase first catalyzes formation of the alpha-hydroxyglycine derivative of the glycine-extended precursor, and the lyase subsequently catalyzes breakdown of the PAM product to the amidated peptide and glyoxylate. We report here the first primary sequence data for PGL, which establish that it is part of the putative protein precursor which also contains PAM. We also show that PAM and PGL activities are colocalized in the secretory granular fraction of neurointermediate pituitary as would be expected for enzymes sharing the same precursor. Time course studies of the amidation reaction using purified soluble pituitary PAM and PGL indicate that both enzymes are essential for enzymatic amidation. Finally, PGL has no effect on the substrate or inhibition kinetics of PAM, and purified pituitary PAM has an acidic pH optimum consistent with its known localization in secretory granules.
Amidine-Lyases↗