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PubMed1989

Retinal melatonin is metabolized within the eye of xenopus laevis.

Retinal synthesis of melatonin, a potent modulator of rhythmic retinal processes, is elevated at night as a result of regulation by a circadian clock. Despite high nocturnal synthetic capacity, both melatonin content and release are low in the retina of the frog Xenopus laevis. We report here that cultured eyecups from Xenopus have the capacity for rapid metabolic breakdown of melatonin. Pharmacological analysis indicates that the initial step in this degradation pathway is deacetylation of melatonin by the enzyme aryl acylamidase (aryl-acylamide amidohydrolase, EC 3.5.1.13). This produces 5-methoxytryptamine, which is then deaminated by monoamine oxidase [amine:oxygen oxidoreductase (deaminating) (flavin-containing), EC 1.4.3.4], producing 5-methoxyindoleacetic acid and 5-methoxytryptophol. Inhibition of aryl acylamidase with eserine dramatically increases the release of endogenous melatonin by eyecups cultured at night, indicating that this pathway is the normal fate of retinal melatonin. Metabolism within the eye suggests a local neuromodulatory role for retinal melatonin, in contrast to the hormonal role of pineal melatonin.

Animals↗

PubMed1997

Biosynthesis, uptake, and degradation of anandamide and palmitoylethanolamide in leukocytes.

Anandamide (arachidonoylethanolamide, AnNH) and palmitoylethanolamide (PEA) have been proposed as the physiological ligands, respectively, of central and peripheral cannabinoid receptors. Both of these receptors are expressed in immune cells, including macrophages and mast cells/basophils, where immunomodulatory and/or anti-inflammatory actions of AnNH and PEA have been recently reported. We now provide biochemical grounds to these actions by showing that the biosynthesis, uptake, and degradation of AnNH and PEA occur in leukocytes. On stimulation with ionomycin, J774 macrophages and RBL-2H3 basophils produced AnNH and PEA, probably through the hydrolysis of the corresponding N-acylphosphatidylethanolamines, also found among endogenous phospholipids. Immunological challenge of RBL-2H3 cells also caused AnNH and PEA release. The chemical structure and the amounts of AnNH and PEA produced upon ionomycin stimulation were determined by means of double radiolabeling experiments and isotope dilution gas chromatography/electron impact mass spectrometry. Both cell lines rapidly sequestered the two amides from the culture medium through temperature-dependent, saturable and chemically inactivable mechanisms. Once uptaken by basophils, AnNH and PEA compete for the same inactivating enzyme which catalyzes their hydrolysis to ethanolamine. This enzyme was found in both microsomal and 10,000 x g fractions of RBL cell homogenates, and exhibited similar inhibition and temperature/pH dependence profiles but a significantly higher affinity for PEA with respect to neuronal "anandamide amidohydrolase." The finding of biosynthetic and inactivating mechanisms for AnNH and PEA in macrophages and basophils supports the previously proposed role as local modulators of immune/inflammatory reactions for these two long chain acylethanolamides.

Amides↗

PubMed1998

Activation and oligomerization of aspartylglucosaminidase.

Secretory, membrane, and lysosomal proteins undergo covalent modifications and acquire their secondary and tertiary structure in the lumen of the endoplasmic reticulum (ER). In order to pass the ER quality control system and become transported to their final destinations, many of them are also assembled into oligomers. We have recently determined the three-dimensional structure of lysosomal aspartylglucosaminidase (AGA), which belongs to a newly discovered family of homologous amidohydrolases, the N-terminal nucleophile hydrolases. Members of this protein family are activated from an inactive precursor molecule by an autocatalytic proteolytic processing event whose exact mechanism has not been thoroughly determined. Here we have characterized in more detail the initial events in the ER required for the formation of active AGA enzyme using transient expression of polypeptides carrying targeted amino acid substitutions. We show that His124 at an interface between two heterodimers of AGA is crucial for the thermodynamically stable oligomeric structure of AGA. Furthermore, the side chain of Thr206 is essential both for the proteolytic activation and enzymatic activity of AGA. Finally, the proper geometry of the residues His204-Asp205 seems to be crucial for the activation of AGA precursor polypeptides. We propose here a reaction mechanism for the activation of AGA which could be valid for homologous enzymes as well.

Amino Acid Sequence↗

PubMed1999

Cloning and characterization of human guanine deaminase. Purification and partial amino acid sequence of the mouse protein.

Mouse erythrocyte guanine deaminase has been purified to homogeneity. The native enzyme was dimeric, being comprised of two identical subunits of approximately 50,000 Da. The protein sequence was obtained from five cyanogen bromide cleavage products giving sequences ranging from 12 to 25 amino acids in length and corresponding to 99 residues. Basic Local Alignment Search Tool (BLAST) analysis of expressed sequence databases enabled the retrieval of a human expressed sequence tag cDNA clone highly homologous to one of the mouse peptide sequences. The presumed coding region of this clone was used to screen a human kidney cDNA library and secondarily to polymerase chain reaction-amplify the full-length coding sequence of the human brain cDNA corresponding to an open reading frame of 1365 nucleotides and encoding a protein of 51,040 Da. Comparison of the mouse peptide sequences with the inferred human protein sequence revealed 88 of 99 residues to be identical. The human coding sequence of the putative enzyme was subcloned into the bacterial expression vector pMAL-c2, expressed, purified, and characterized as having guanine deaminase activity with a Km for guanine of 9.5 +/- 1.7 microM. The protein shares a 9-residue motif with other aminohydrolases and amidohydrolases (PGX[VI]DXH[TVI]H) that has been shown to be ligated with heavy metal ions, commonly zinc. The purified recombinant guanine deaminase was found to contain approximately 1 atom of zinc per 51-kDa monomer.

Amino Acid Sequence↗

PubMed2006

Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1).

Embryonic factor 1 (FAC1) is one of the earliest expressed plant genes and encodes an AMP deaminase (AMPD), which is also an identified herbicide target. This report identifies an N-terminal transmembrane domain in Arabidopsis FAC1, explores subcellular fractionation, and presents a 3.3-A globular catalytic domain x-ray crystal structure with a bound herbicide-based transition state inhibitor that provides the first glimpse of a complete AMPD active site. FAC1 contains an (alpha/beta)(8)-barrel characterized by loops in place of strands 5 and 6 that places it in a small subset of the amidohydrolase superfamily with imperfect folds. Unlike tetrameric animal orthologs, FAC1 is a dimer and each subunit contains an exposed Walker A motif that may be involved in the dramatic combined K(m) (25-80-fold lower) and V(max) (5-6-fold higher) activation by ATP. Normal mode analysis predicts a hinge motion that flattens basic surfaces on each monomer that flank the dimer interface, which suggests a reversible association between the FAC1 globular catalytic domain and intracellular membranes, with N-terminal transmembrane and disordered linker regions serving as the anchor and attachment to the globular catalytic domain, respectively.

AMP Deaminase↗

PubMed1995

Intracellular sorting of aspartylglucosaminidase: the role of N-linked oligosaccharides and evidence of Man-6-P-independent lysosomal targeting.

Aspartylglucosaminidase (AGA, E.C. 3.5.1.26) is a soluble lysosomal hydrolase that participates in the degradation of glycoproteins. Here we analyzed the special features in the intracellular targeting of this dimeric amidohydrolase, especially the role of N-linked sugars and their phosphorylation in transport and activity of heterodimeric aspartylglucosaminidase, using in vitro mutagenesis and transient expression of mutant polypeptides in COS cells. The single N-glycosylation sites of both the alpha and beta subunits were destroyed individually and in combination. Just one remaining N-glycosylation site on either subunit was sufficient for normal processing into subunits and lysosomal transport, but the totally nonglycosylated enzyme, although active and processed into subunits, was not transported into lysosomes and became trapped in the endoplasmic reticulum (ER) or secreted. The intracellular targeting of AGA was partially disturbed by the lack of glycosylation in the beta subunit, resulting in accumulation of dimeric, active polypeptides in the ER, whereas lack of oligosaccharides in the alpha subunit did not affect the intracellular targeting of AGA. N-glycans in the beta subunit were found to be essential for the long-term stability of the polypeptide in the cell, but not for initial folding or subunit processing into the active dimeric molecule. Both subunits have two glycosylation isoforms. Both forms of the alpha subunit were found to be phosphorylated, whereas only one of the two glycosylation isoforms of the beta subunit is phosphorylated. The mutant enzyme with nonglycosylated alpha subunit and nonphosphorylated beta subunit is transported into lysosomes, suggesting that AGA is capable of using an alternative, mannose-6-phosphate receptor-independent routing into lysosomes.

Aspartylglucosylaminase↗

PubMed2006

Automated discovery of 3D motifs for protein function annotation.

MOTIVATION: Function inference from structure is facilitated by the use of patterns of residues (3D motifs), normally identified by expert knowledge, that correlate with function. As an alternative to often limited expert knowledge, we use machine-learning techniques to identify patterns of 3-10 residues that maximize function prediction. This approach allows us to test the assumption that residues that provide function are the most informative for predicting function. RESULTS: We apply our method, GASPS, to the haloacid dehalogenase, enolase, amidohydrolase and crotonase superfamilies and to the serine proteases. The motifs found by GASPS are as good at function prediction as 3D motifs based on expert knowledge. The GASPS motifs with the greatest ability to predict protein function consist mainly of known functional residues. However, several residues with no known functional role are equally predictive. For four groups, we show that the predictive power of our 3D motifs is comparable with or better than approaches that use the entire fold (Combinatorial-Extension) or sequence profiles (PSI-BLAST). AVAILABILITY: Source code is freely available for academic use by contacting the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗

PubMed1999

Schizosaccharomyces pombe produces novel Gal0-2Man1-3 O-linked oligosaccharides.

Schizosaccharomyces pombe whole-cell glycoproteins, previously depleted of N-linked glycans by sequential treatment with endo-ss-N-acetylglucosaminidase H and peptide-N4-asparagine amidohydrolase F, were ss-eliminated with 0.1 M NaOH/1 M NaBH4 to release the O-linked oligosaccharides. The saccharide-alditols were separated by gel-exclusion chromatography into pools from Hexitol to Hex4Hexitol in size. Analysis of the Hexitol pool indicated Man to be the only sugar linked to Ser or Thr residues. The Hex1Hexitol pool contained two components, Galalpha1,2Man-ol (2A) and Manalpha1, 2Man-ol (2B). The Hex2Hexitol pool contained two components, Galalpha1,2Manalpha1,2Man-ol (3A) and Manalpha1,2Manalpha1,2Man-ol (3B). The two Hex3Hexitol components were Galalpha1,2(Galalpha1, 3)Manalpha1,2Man-ol (4A) and Manalpha1,2(Galalpha1,3)Manalpha1, 2Man-ol (4B). The Hex4Hexitol component was found to be a single isomer with the composition of Galalpha1,2(Galalpha1,3)Manalpha1, 2Manalpha1,2Man-ol (5AB). Surprisingly, galactobiose was not detected in any of these oligosaccharides. The gma12 (T. G. Chappell and G. Warren (1989) J. Cell Biol., 109, 2693-2707) and gth1 (T. G. Chappell personal communication) alpha1, 2-galactosyltransferase-deficient mutants and the gma12/gth1 double mutant S.pombe strains were similarly examined. The results indicated that gma12p is solely responsible for the addition of terminal alpha1,2-linked Gal in compound 2A, while one or both of gma12p and gth1p are required for the alpha1,2-linked Gal in 4A. Both transferases are largely responsible for terminal Gal in isomer 5AB. Neither gma12 nor gth1 had any discernible effect on the structure of the large N-linked galactomannans as determined by 1H NMR spectroscopy. Thus, while gth1p and gma12p appear responsible for adding alpha1,2-linked Gal to terminal Man, neither adds galactose side chains to the N-linked poly alpha1,6-Man outerchain, nor the O-linked branch-forming alpha1,3-linked Gal. Furthermore, the presence of Hexalpha1,2(Galalpha1,3)Manalpha1,2- structures in the O-linked glycans implies the presence of a novel branch-forming alpha1,3-galactosyltransferase in S.pombe.

Carbohydrate Conformation↗

PubMed1995

Determination of amounts of polyamines excreted in urine: demonstration of N1,N8-diacetylspermidine and N1,N12-diacetylspermine as components commonly occurring in normal human urine.

An analytical system developed for fractionating free and monoacetylated polyamines [Hiramatsu, K. et al. (1994) J. Biochem. 115, 584-589] was proved useful also in detecting diacetylpolyamines, namely N1,N8-diacetylspermidine (diAcSpd) and N1,N12-diacetylspermine (diAcSpm). Detection limits were 0.9 and 0.6 pmol (S/N = 5) for diAcSpd and diAcSpm, respectively. Analytical recovery and within-run variation were also satisfactory. Human urine samples were found to contain diAcSpd and diAcSpm. These polyamines were identified on the basis of the following observations: (i) their retention times were coincident with those of authentic samples; (ii) they were deacetylated to N8-acetylspermidine and monoacetyl- and free spermine, respectively, by acetylpolyamine amidohydrolase; and (iii) they were practically inert to direct oxidation by bacterial polyamine oxidase as were authentic samples. The amounts of eleven polyamine species including diAcSpd and diAcSpm in urine samples from 52 healthy persons were determined. Mean values for the major polyamine components were consistent with those reported by others. Although the amounts of diAcSpd and diAcSpm were very small, comprising only 1.4 and 0.46% of total polyamines, respectively, these two compounds were found to be always present in healthy human urine as regular constituents. Moreover, variation in their content among individuals was small, suggesting that excretion of these components in urine is strictly regulated.

Biogenic Polyamines↗

PubMed2005

Coronary vasodilator effects of endogenous cannabinoids in vasopressin-preconstricted unpaced rat isolated hearts.

The mechanisms by which cannabinoids alter coronary vascular tone and cardiac performance are controversial. We investigated the effects of various cannabinoids in spontaneously beating Langendorff-perfused rat hearts. Bolus injections of anandamide (0.1-1 micromol) caused no change in coronary flow (CF) or left ventricular systolic pressure (LVSP). In hearts preperfused with vasopressin to induce vasoconstrictor tone, anandamide or the selective CB1 receptor agonist ACEA (1-100 nmol) dose-dependently increased CF by up to 267% and LVSP by 20 mm Hg. The metabolically stable endocannabinoid derivatives, R-methanandamide and noladin ether, displayed similar effects. In contrast, Delta-THC (10-100 nmol), the major psychoactive ingredient of cannabis, strongly decreased CF and LVSP. The CB2 receptor agonist JWH-133 (10-100 nmol) elicited vasodilator and positive inotropic effects only at higher doses. The CB1 antagonists SR141716A and AM-251 as well as the potassium channel inhibitors tetraethylammonium and iberiotoxin blocked the anandamide-induced increases in CF and LVSP, whereas the CB2 antagonist SR144528 and the putative "CB3 antagonist" O-1918 did not have an inhibitory effect. Immunohistochemistry revealed the presence of cardiac CB1 but no CB2 receptors. Anandamide and 2-arachidonoylglycerol were detected in heart tissue. However, combined application of fatty acid amidohydrolase inhibitors and the transport inhibitor AM-404 to augment tissue levels of endocannabinoids was without effect on CF or LVSP. We conclude that in the rat isolated heart with reestablished vasoconstrictor tone, cannabinoids including anandamide elicit coronary vasodilation and a secondary increase in contractility via CB1 receptors and potassium channels.

Animals↗

PubMed1990

Characterization and partial purification of L-asparaginase from Corynebacterium glutamicum.

A high L-asparaginase (L-asparagine amidohydrolase: EC 3.5.1.1) activity was found under conditions of lysine overproduction in cultures of Corynebacterium glutamicum. L-Asparaginase was purified 98-fold by protamine sulphate precipitation. DEAE-Sephacel anion exchange, ammonium sulphate precipitation and Sephacryl S-200 gel filtration. The asparaginase protein was subjected to PAGE under non-denaturing conditions, identified by an in situ reaction and eluted from the gel in an active form. The estimated Mr from gel filtration and SDS-PAGE was 80,000. The L-asparaginase activity was inhibited by the L-asparagine analogue 5-diazo-4-oxo-L-norvaline. Neither D-asparagine nor L-glutamine was a substrate for the enzyme. L-Asparaginase was produced constitutively: its role may be that of an overflow enzyme, converting excess asparagine into aspartic acid, the direct precursor of lysine and threonine.

Asparaginase↗

PubMed1998

N-Acylethanolamines: formation and molecular composition of a new class of plant lipids

Recently, the biosynthesis of an unusual membrane phospholipid, N-acylphosphatidylethanolamine (NAPE), was found to increase in elicitor-treated tobacco (Nicotiana tabacum L.) cells (K.D. Chapman, A. Conyers-Hackson, R.A. Moreau, S. Tripathy [1995] Physiol Plant 95: 120-126). Here we report that before induction of NAPE biosynthesis, N-acylethanolamine (NAE) is released from NAPE in cultured tobacco cells 10 min after treatment with the fungal elicitor xylanase. In radiolabeling experiments [14C]NAE (labeled on the ethanolamine carbons) increased approximately 6-fold in the culture medium, whereas [14C]NAPE associated with cells decreased approximately 5-fold. Two predominant NAE molecular species, N-lauroylethanolamine and N-myristoylethanolamine, were specifically identified by gas chromatography-mass spectrometry in lipids extracted from culture medium, and both increased in concentration after elicitor treatment. NAEs were found to accumulate extracellularly only. A microsomal phospholipase D activity was discovered that formed NAE from NAPE; its activity in vitro was stimulated about 20-fold by mastoparan, suggesting that NAPE hydrolysis is highly regulated, perhaps by G-proteins. Furthermore, an NAE amidohydrolase activity that catalyzed the hydrolysis of NAE in vitro was detected in homogenates of tobacco cells. Collectively, these results characterize structurally a new class of plant lipids and identify the enzymatic machinery involved in its formation and inactivation in elicitor-treated tobacco cells. Recent evidence indicating a signaling role for NAPE metabolism in mammalian cells (H.H.O. Schmid, P.C. Schmid, V. Natarajan [1996] Chem Phys Lipids 80: 133-142) raises the possibility that a similar mechanism may operate in plant cells.

Journal Article↗

PubMed1983

Subcellular localization of rice leaf aryl acylamidase activity.

The intracellular localization of aryl acylamidase (aryl-acylamide amidohydrolase, EC 3.5.1.13) in rice (Oryza sativa L. var Starbonnet) leaves was investigated. The enzyme hydrolyzes and detoxifies the herbicide propanil (3,4-dichloropropionanilide) thereby accounting for immunity of the rice plant to herbicidal action. Fractionation of mesophyll protoplasts by differential centrifugation yielded the highest specific activity of amidase in the crude mitochondrial fraction. Further separation of density gradients of the silica sol Percoll also indicated that this enzyme was mitochondrial. By the use of biochemical markers, the purified mitochondrial fraction was shown to be substantially free of contamination from nuclei, chloroplasts, golgi, and plasma membranes. Subfractionation of the purified mitochondria suggests that this enzyme is located on the outer membrane.

Journal Article↗

PubMed1987

Ureide Catabolism of Soybeans : II. Pathway of Catabolism in Intact Leaf Tissue.

Allantoin catabolism studies have been extended to intact leaf tissue of soybean (Glycine max L. Merr.). Phenyl phosphordiamidate, one of the most potent urease inhibitors known, does not inhibit (14)CO(2) release from [2,7-(14)C]allantoin (urea labeled), but inhibits urea dependent CO(2) release >/=99.9% under similar conditions. Furthermore, (14)CO(2) and [(14)C] allantoate are the only detectable products of [2,7-(14)C]allantoin catabolism. Neither urea nor any other product were detected by analysis on HPLC organic acid or organic base columns although urea and all commercially available metabolites that have been implicated in allantoin and glyoxylate metabolism can be resolved by a combination of these two columns. In contrast, when allantoin was labeled in the two central, nonureido carbons ([4,5-(14)C]allantoin), its catabolism to [(14)C]allantoate, (14)CO(2), [(14)C]glyoxylate, [(14)C]glycine, and [(14)C]serine in leaf discs could be detected. These data are fully consistent with the metabolism of allantoate by two amidohydrolase reactions (neither of which is urease) that occur at similar rates to release glyoxylate, which in turn is metabolized via the photorespiratory pathway. This is the first evidence that allantoate is metabolized without urease action to NH(4) (+) and CO(2) and that carbons 4 and 5 enter the photorespiratory pathway.

Journal Article↗

PubMed1988

Amino Acid Metabolism of Lemna minor L. : III. Responses to Aminooxyacetate.

Aminooxyacetate, a known inhibitor of transaminase reactions and glycine decarboxylase, promotes rapid depletion of the free pools of serine and aspartate in nitrate grown Lemna minor L. This compound markedly inhibits the methionine sulfoximine-induced accumulation of free ammonium ions and greatly restricts the methionine sulfoximine-induced depletion of amino acids such as glutamate, alanine, and asparagine. These results suggest that glutamate, alanine, and asparagine are normally catabolized to ammonia by transaminase-dependent pathways rather than via dehydrogenase or amidohydrolase reactions. Aminooxyacetate does not inhibit the methionine sulfoximine-induced irreversible deactivation of glutamine synthetase in vivo, indicating that these effects cannot be simply ascribed to inhibition of methionine sulfoximine uptake by amino-oxyacetate. This transaminase inhibitor promotes extensive accumulation of several amino acids including valine, leucine, isoleucine, alanine, glycine, threonine, proline, phenylalanine, lysine, and tyrosine. Since the aminooxyacetate induced accumulations of valine, leucine, and isoleucine are not inhibited by the branched-chain amino acid biosynthesis inhibitor, chlorsulfuron, these amino acid accumulations most probably involve protein turnover. Depletions of soluble protein bound amino acids are shown to be approximately stoichiometric with the free amino acid pool accumulations induced by aminooxyacetate. Aminooxyacetate is demonstrated to inhibit the chlorsulfuron-induced accumulation of alpha-amino-n-butyrate in L. minor, supporting the notion that this amino acid is derived from transamination of 2-oxobutyrate.

Journal Article↗

PubMed2000

Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded by the Escherichia coli genome.

A new Escherichia coli L-asparaginase belonging to the class of Ntn amidohydrolases has been crystallized using the vapour-diffusion method and PEG 4000 as the precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1) (unit-cell parameters a = 50. 3, b = 77.6, c = 148.2 A) and diffract to 1.65 A resolution. The structure has been solved by molecular replacement using aspartylglucosaminidase from Flavobacterium meningosepticum as the search model. The asymmetric unit contains four protein chains composed into a dimer of alphabeta heterodimers, where the subunits alpha and beta are the product of autoproteolytic cleavage of the immature protein.

Amino Acid Sequence↗

PubMed1997

A new crystal form of penicillin acylase from Escherichia coli.

A new crystal form of penicillin acylase (penicillin amidohydrolase, E.C. 3.5.1.11) from Escherichia coli W (ATCC 11105) is reported. The crystals were grown using a combination of hanging-drop and streak-seeding methods. The crystals are in the monoclinic space group P2(1) with cell dimensions a = 51.52, b = 131.95, c = 64.43 A, beta = 106.12 degrees. There is one heterodimer in the asymmetric unit (V(m) = 2.45 A(3) Da(-1)) and the solvent content is 49%. Preliminary data have been collected to d(min) = 2.7 A using a MAR Research image plate and a rotating-anode X-ray source. Subsequent experiments show diffraction beyond 1.3 A at a synchrotron radiation source.

Journal Article↗

PubMed1999

Crystallization of a precursor penicillin acylase from Escherichia coli.

The crystallization of a mutant precursor penicillin acylase [penicillin amidohydrolase (amidase) E.C. 3.5.1.11] from Escherichia coli W (ATCC 11105) using the hanging-drop method is reported. The crystals are in space group P1 with unit-cell parameters a = 51.04, b = 63.58, c = 71.17 A, alpha = 103.0, beta = 110.6, gamma = 105.3 degrees, with one molecule in the asymmetric unit, and diffract to 1. 8 A using synchrotron radiation.

Bacterial Proteins↗