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Mendel Tuchman

Publications and source records attributed to Mendel Tuchman.

At least 19 recordsLinked to original sources
PubMed2006

Expression, crystallization and preliminary crystallographic studies of a novel bifunctional N-acetylglutamate synthase/kinase from Xanthomonas campestris homologous to vertebrate N-acetylglutamate synthase.

A novel N-acetylglutamate synthase/kinase bifunctional enzyme of arginine biosynthesis that was homologous to vertebrate N-acetylglutamate synthases was identified in Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the hexagonal space group P6(2)22, with unit-cell parameters a = b = 134.60, c = 192.11 A, and diffract to about 3.0 A resolution. Selenomethionine-substituted recombinant protein was produced and selenomethionine substitution was verified by mass spectroscopy. Multiple anomalous dispersion (MAD) data were collected at three wavelengths at SER-CAT, Advanced Photon Source, Argonne National Laboratory. Structure determination is under way using the MAD phasing method.

Amino-Acid N-Acetyltransferase↗
PubMed2006

Structures of N-acetylornithine transcarbamoylase from Xanthomonas campestris complexed with substrates and substrate analogs imply mechanisms for substrate binding and catalysis.

N-acetyl-L-ornithine transcarbamoylase (AOTCase) is a new member of the transcarbamoylase superfamily that is essential for arginine biosynthesis in several eubacteria. We report here crystal structures of the binary complexes of AOTCase with its substrates, carbamoyl phosphate (CP) or N-acetyl-L-ornithine (AORN), and the ternary complex with CP and N-acetyl-L-norvaline. Comparison of these structures demonstrates that the substrate-binding mechanism of this novel transcarbamoylase is different from those of aspartate and ornithine transcarbamoylases, both of which show ordered substrate binding with large domain movements. CP and AORN bind to AOTCase independently, and the main conformational change upon substrate binding is ordering of the 80's loop, with a small domain closure around the active site and little movement of the 240's loop. The structures of the complexes provide insight into the mode of substrate binding and the mechanism of the transcarbamoylation reaction.

Binding Sites↗
PubMed2006

Structure of a novel N-acetyl-L-citrulline deacetylase from Xanthomonas campestris.

The structure of a novel acetylcitrulline deacetylase from the plant pathogen Xanthomonas campestris has been solved by multiple-wavelength anomalous dispersion (MAD) using crystals grown from selenomethionine-substituted protein and refined at 1.75 A resolution. The asymmetric unit of the crystal contains one monomer consisting of two domains, a catalytic domain and a dimerization domain. The catalytic domain is able to bind a single Co(II) ion at the active site with no change in conformation. The dimerization domain forms an interface between two monomers related by a crystallographic two-fold symmetry axis. The interface is maintained by hydrophobic interactions between helices and hydrogen bonding between two beta strands that form a continuous beta sheet across the dimer interface. Because the dimers are also related by two-fold crystallographic axes, they pack together across the crystal via the dimerization domain, suggesting that higher order oligomers may form in solution. The polypeptide fold of the monomer is similar to the fold of Pseudomonas sp. carboxypeptidase G2 and Neisseria meningitidis succinyl diaminopimelate desuccinylase. Structural comparison among these enzymes allowed modeling of substrate binding and suggests a possible catalytic mechanism, in which Glu130 functions as a bifunctional general acid-base catalyst and the metal ion polarizes the carbonyl of the acetyl group.

Amidohydrolases↗
PubMed2006

Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis.

A Bacteroides fragilis gene (argF'(bf)), the disruption of which renders the bacterium auxotrophic for arginine, was expressed and its recombinant protein purified and studied. The novel protein catalyzes the carbamylation of N-succinyl-L-ornithine but not L-ornithine or N-acetyl-L-ornithine, forming N-succinyl-L-citrulline. Crystal structures of this novel transcarbamylase complexed with carbamyl phosphate and N-succinyl-L-norvaline, as well as sulfate and N-succinyl-L-norvaline have been determined and refined to 2.9 and 2.8 A resolution, respectively. They provide structural evidence that this protein is a novel N-succinyl-L-ornithine transcarbamylase. The data provided herein suggest that B. fragilis uses N-succinyl-L-ornithine rather than N-acetyl-L-ornithine for de novo arginine biosynthesis and therefore that this pathway in Bacteroides is different from the canonical arginine biosynthetic pathway of most organisms. Comparison of the structures of the new protein with those recently reported for N-acetyl-L-ornithine transcarbamylase indicates that amino acid residue 90 (B. fragilis numbering) plays an important role in conferring substrate specificity for N-succinyl-L-ornithine versus N-acetyl-L-ornithine. Movement of the 120 loop upon substrate binding occurs in N-succinyl-L-ornithine transcarbamylase, while movement of the 80 loop and significant domain closure take place as in other transcarbamylases. These findings provide new information on the putative role of succinylated intermediates in arginine biosynthesis and on the evolution of transcarbamylases.

Acyltransferases↗
PubMed2006

Mutations and polymorphisms in the human ornithine transcarbamylase (OTC) gene.

Ornithine transcarbamylase (OTC) deficiency is the most common inherited disorder of the urea cycle and is transmitted as an X-linked trait. Defects in the OTC gene cause a block in ureagenesis resulting in hyperammonemia, which can lead to brain damage and death. Three previous mutation updates for the OTC gene have been published, in 1993, 1995, and 2002. The most recent comprehensive update, in 2002, contained 244 mutations including 13 nondisease-causing mutations and polymorphisms. This current update reports 341 mutations, of which 93 have not been previously reported, and an additional 29 nondisease-causing mutations and polymorphisms. Out of the 341 mutations, 149 were associated with neonatal onset of hyperammonemia (within the first week of life), 70 were seen in male patients with later onset of hyperammonemia, and 121 were found in heterozygous females (one unknown). Along with the reported mutations, residual enzyme activities and other pertinent clinical information are included whenever available. Most mutations in the OTC gene are specific to a particular family ("private" mutations). They are distributed throughout the gene, with a significant paucity of mutations in the 32 first codons encoding the "leader" peptide (exon 1 and the beginning of exon 2). Almost all mutations in consensus splice sites confer a neonatal onset phenotype. Using the current molecular screening methods, mutations are found in about 80% of the patients. The remaining patients may have mutations in regulatory domains or mutations deep in the introns, which constitute 98.5% of the genomic sequence. In addition, a phenocopy of OTC deficiency caused by mutations in another unknown gene cannot be excluded.

Amino Acid Sequence↗
PubMed2006

Biochemical properties of recombinant human and mouse N-acetylglutamate synthase.

N-Acetylglutamate synthase (NAGS, EC 2.3.1.1) is a mitochondrial enzyme that catalyzes the formation of N-acetylglutamate (NAG) from glutamate and acetylcoenzyme A. NAG is an obligatory activator of carbamylphosphate I (CPSI), the first and a rate limiting enzyme of ureagenesis. The enzymatic activity of NAGS increases in the presence of arginine. Since the level of NAGS activity depends on the concentrations of two amino acids, glutamate and arginine, and it supplies the essential cofactor for CPSI, NAGS may play an important role in the regulation of ureagenesis. The amino acid sequences of human and mouse NAGS consist of three regions with different degrees of conservation: the mitochondrial targeting signal (MTS), the variable domain, and the conserved domain. Removal of the MTS results in mature NAGS (NAGS-M) while removal of the MTS and the variable domain results in conserved NAGS (NAGS-C). The biochemical properties of purified recombinant human and mouse NAGS-M and NAGS-C were determined in this study with the goal of better understanding the role of the variable domain in NAGS function. The activity of all four proteins doubled in the presence of arginine, while the affinities for substrates changed less than two fold. The turnover numbers of NAGS-C are double those of NAGS-M proteins. Processing of NAGS-M to form NAGS-C results in an enzyme with higher catalytic activity and could play a role in the regulation of NAG production, CPSI function, and urea synthesis.

Amino-Acid N-Acetyltransferase↗
PubMed2006

Acetylornithine transcarbamylase: a novel enzyme in arginine biosynthesis.

Ornithine transcarbamylase is a highly conserved enzyme in arginine biosynthesis and the urea cycle. In Xanthomonas campestris, the protein annotated as ornithine transcarbamylase, and encoded by the argF gene, is unable to synthesize citrulline directly from ornithine. We cloned and overexpressed this X. campestris gene in Escherichia coli and show that it catalyzes the formation of N-acetyl-L-citrulline from N-acetyl-L-ornithine and carbamyl phosphate. We now designate this enzyme as an acetylornithine transcarbamylase. The K(m) values for N-acetylornithine and carbamyl phosphate were 1.05 mM and 0.01 mM, respectively. Additional putative transcarbamylases that might also be misannotated were found in the genomes of members of other xanthomonads, Cytophaga, and Bacteroidetes as well as in DNA sequences of bacteria from environmental isolates. It appears that these different paths for arginine biosynthesis arose very early in evolution and that the canonical ornithine transcarbamylase-dependent pathway became the prevalent form. A potent inhibitor, N(alpha)-acetyl-N(delta)-phosphonoacetyl-L-ornithine, was synthesized and showed a midpoint of inhibition at approximately 22 nM; this compound may prove to be a useful starting point for designing inhibitors specific to this novel family of transcarbamylases.

Arginine↗
PubMed2005

The use of yeast mitochondria to study the properties of wild-type and mutant human mitochondrial ornithine transporter.

Yeast deletion models have general utility for the study of a variety of inherited metabolic disorders. Mutations in the mitochondrial ornithine transporter result in hyperammonemia, hyperornithinemia, homocitrullinuria syndrome, a disorder of the urea cycle. To study the effects of mutations in a model system that more closely resembles the in vivo environment, we have developed an expression system based on a yeast strain lacking its endogenous ornithine transporter homologue. Wild-type human ornithine transporter and a recurrent mutation, DeltaF 188, were expressed and characterized with this system. The wild-type transporter appeared to insert into yeast mitochondria in the same orientation as in mammalian mitochondria. It showed stereospecificity, strong antiport activity and ornithine transport was competed by citrulline and arginine. The DeltaF 188 mutant was not incorporated into the membrane to the same extent as wild type, but retained significant residual activity and lost stereospecificity. In these isolated mitochondria, samarium chloride was found to be a potent blocker of transport compared to previously reported sulfhydryl-based inhibitors. A low-affinity background transport activity that promoted the exchange of ornithine for either acidic or basic amino acids was observed. This yeast model can readily be extended to the study of protein:protein interactions. In this manner, the use of yeast deletion strains can serve as a general framework to perform metabolic pathway analysis.

Amino Acid Transport Systems, Basic↗
PubMed2005

Health and economic benefits of well-designed evaluations: some lessons from evaluating neuroblastoma screening.

BACKGROUND: Well-designed evaluations of health services are frequently made today. However, the extent of the evaluations' benefits and costs is not well documented, creating uncertainty whether their use is optimal from society's perspective. We examined these costs and benefits using data from one well-designed evaluation, the Quebec Neuroblastoma Screening Project (QNSP). It screened most Quebec newborns between 1989 and 1994 for neuroblastoma. As previously reported, the screening did not reduce neuroblastoma mortality and caused adverse health effects. METHODS: We compared the cost of doing the QNSP with its benefits. Had the QNSP not been undertaken, neuroblastoma screening would have been implemented throughout North America. We assume that screening would have started in 1989 and ended in 2002. The QNSP's benefits include the health costs and adverse health effects averted by not using ineffective screening during those 14 years. In our calculations we used neuroblastoma incidence data for the QNSP and for Ontario where there was no screening, detailed data describing the health services used by the patients, and Quebec cost data for those services. RESULTS: The QNSP cost 8.77 million dollars (2002 US dollars). By not implementing similar screening programs between 1989 and 2002, the United States and Canada avoided 574.1 million dollars in health costs, the unnecessary treatment of 9223 children, and false-positive findings for 5003 children screened. CONCLUSIONS: The health care costs and adverse health effects averted by the QNSP justify its costs. These results show that well-designed evaluations can yield--at least sometimes--benefits substantially greater than their high costs. This raises an important policy issue: are these evaluations now being under- or over used?

Canada↗
PubMed2005

Expression, purification, crystallization and preliminary X-ray crystallographic studies of a novel acetylcitrulline deacetylase from Xanthomonas campestris.

A novel N-acetyl-L-citrulline deacetylase that is able to catalyze the hydrolysis of N-acetyl-L-citrulline to acetate and citrulline was identified from Xanthomonas campestris. The protein was overexpressed, purified and crystallized. The crystals belong to the monoclinic space group C2 and diffract to 1.75 A resolution, with unit-cell parameters a = 94.13, b = 95.23, c = 43.61 A, beta = 93.76 degrees. Since attempts to use homologous structural models to solve the structure via molecular replacement were unsuccessful, the selenomethionine-substituted protein was prepared using an overnight auto-induction overexpression system. Selenomethionine incorporation into the protein was verified by MALDI-TOF/TOF mass-spectroscopic analysis after trypsin digestion. The crystals of the selenomethionine-substituted protein were prepared using crystallization conditions similar to those for the native protein. Multiple anomalous dispersion (MAD) data were collected at Brookhaven National Laboratory. Structure determination is under way using the MAD phasing method.

Amidohydrolases↗
PubMed2005

Crystal structure of N-acetylornithine transcarbamylase from Xanthomonas campestris: a novel enzyme in a new arginine biosynthetic pathway found in several eubacteria.

We have identified in Xanthomonas campestris a novel N-acetylornithine transcarbamylase that replaces ornithine transcarbamylase in the canonic arginine biosynthetic pathway of several Eubacteria. The crystal structures of the protein in the presence and absence of the reaction product, N-acetylcitrulline, were determined. This new family of transcarbamylases lacks the DxxSMG motif that is characteristic of all ornithine transcarbamylases (OTCases) and contains a novel proline-rich loop that forms part of the active site. The specificity for N-acetylornithine is conferred by hydrogen bonding with residues in the proline-rich loop via water molecules and by hydrophobic interactions with residues from the adjacent 80's, 120's, and proline-rich loops. This novel protein structure provides a starting point for rational design of specific analogs that may be useful in combating human and plant pathogens that utilize acetylornithine transcarbamylase rather than ornithine transcarbamylase.

Binding Sites↗
PubMed2005

Late onset N-acetylglutamate synthase deficiency caused by hypomorphic alleles.

N-acetylglutamate (NAG) is a unique cofactor that is essential for the conversion of ammonia to urea in the liver. N-acetylglutamate synthase (NAGS) catalyzes the formation of NAG. Deficiency of NAGS causes a block in ureagenesis resulting in hyperammonemia. Although a number of mutations have been identified in the NAGS gene, their effects on NAGS enzymatic activity have not been examined. We describe here three mutations in two families with NAGS deficiency. Studies of the purified recombinant mutant proteins revealed deleterious effects on NAGS affinity for substrates, and on the rate of catalysis. These studies provide a better understanding of the function of NAGS, and the mechanisms for deleterious effect of mutations causing inherited NAGS deficiency.

Adult↗
PubMed2005

Management and outcome of neonatal-onset ornithine transcarbamylase deficiency following liver transplantation at 60 days of life.

Neonatal hyperammonemia secondary to X-linked ornithine transcarbamylase (OTC) deficiency carries a high risk of morbidity and mortality. Results of medical therapy are less than satisfactory. Experience with liver transplantation in very young affected infants is limited. We report a male newborn with severe OTC deficiency who underwent successful orthotopic, cadaveric liver transplantation at the age of 60 days. Although technically challenging in the neonatal period, liver transplantation should be considered early as the most promising treatment approach currently available.

Brain↗
PubMed2004

Restoration of ureagenesis in N-acetylglutamate synthase deficiency by N-carbamylglutamate.

In a patient with N-acetylglutamate synthase (NAGS) deficiency, incorporation of an isotopic label from ammonium chloride into urea was markedly reduced before treatment with N-carbamyl-L-glutamate (NCLG) and completely normalized following treatment. Blood ammonia rose following ammonium tracer ingestion before treatment but remained low following treatment. Serum urea concentration doubled following the treatment.

Acetyltransferases↗
PubMed2004

Mammalian N-acetylglutamate synthase.

N-Acetylglutamate synthase (NAGS, E.C. 2.3.1.1) is a mitochondrial enzyme that catalyzes the formation of N-acetylglutamate (NAG), an essential allosteric activator of carbamylphosphate synthetase I (CPSI). The mouse and human NAGS genes have been identified based on similarity to regions of NAGS from Neurospora crassa and cloned from liver cDNA libraries. These genes were shown to complement an argA- (NAGS) deficient Escherichia coli strain, and enzymatic activity of the proteins was confirmed by a new stable isotope dilution assay. The deduced amino acid sequence of mammalian NAGS contains a putative mitochondrial-targeting signal at the N-terminus. The mouse NAGS preprotein was overexpressed in insect cells to determine post-translational modifications and two processed proteins with different N-terminal truncations have been identified. Sequence analysis using a hidden Markov model suggests that the vertebrate NAGS protein contains domains with a carbamate kinase fold and an acyl-CoA N-acyltransferase fold, and protein crystallization experiments are currently underway. Inherited NAGS deficiency results in hyperammonemia, presumably due to the loss of CPSI activity. We, and others, have recently identified mutations in families with neonatal and late-onset NAGS deficiency and the identification of the gene has now made carrier testing and prenatal diagnosis feasible. A structural analog of NAG, carbamylglutamate, has been shown to bind and activate CPSI, and several patients have been reported to respond favorably to this drug (Carbaglu).

Acetyltransferases↗
PubMed2004

Pharmacokinetics of sodium phenylacetate and sodium benzoate following intravenous administration as both a bolus and continuous infusion to healthy adult volunteers.

BACKGROUND: Ammunol (sodium phenylacetate/sodium benzoate) is an intravenously administered, investigational drug used for the treatment of acute hyperammonemia in infants, children, and adults with urea cycle enzyme deficiencies. A pharmacokinetic study of sodium phenylacetate/sodium benzoate (NAPA/NABZ) was performed in two groups of normal healthy volunteers, following the dosing regimen used to treat hyperammonemia. METHODS: The first group of subjects (n = 3) received a bolus dose of 5.5 g/m2 of NAPA/NABZ, over a period of 1.5 h. Following a seven-day washout, subjects then received the same bolus dose, followed by a continuous infusion of 5.5 g/m2 over 24h. A second group of different subjects (n = 17) received the same treatment regimen, but using doses of 3.75 g/m2. Phenylacetate (PA) and benzoate (BZ), and their respective metabolites, phenylacetylglutamine (PAG), and hippurate (HIP) were measured over a 24-h period. An HPLC method was used for the measurement of all analyte concentrations. Non-compartmental analysis and modeling was performed using WinNonlin Professional. RESULTS: Both BZ and PA displayed saturable, non-linear elimination, with a decrease in clearance with increased dose. During the bolus dose with continuous infusion regimen, plasma levels of both BZ and PA peaked at the end of the priming dose, and PA levels remained near peak for 5-9h. In contrast, BZ plasma levels immediately fell following the priming dose, and became undetectable at 14.1+/-4.2 and 26.8+/-2.3h in the low- and high-dose group, respectively. The formation of HIP occurred more rapidly than that of PAG. For both PA and BZ, metabolite formation increased in a linear fashion with the dose. CONCLUSION: These data describe the pharmacokinetics of PA and BZ, and their respective metabolites, as observed in healthy adult volunteers, with the higher dose studied equivalent to that used to treat hyperammonemia. Dose optimization is required to maximize nitrogen removal, while minimizing the risk of toxicity, especially due to PA. Because of the slower elimination of PA, and the non-linear pharmacokinetic behavior displayed by both PA and BZ, only investigational protocol-specific doses should be used, and higher doses should be avoided unless blood level monitoring can be done promptly and frequently.

Administration, Oral↗
PubMed2003

Significant behavioral disturbances in succinic semialdehyde dehydrogenase (SSADH) deficiency (gamma-hydroxybutyric aciduria).

We report two adult patients with succinic semialdehyde dehydrogenase deficiency, manifesting as gamma-hydroxybutyric aciduria. For both, the clinical presentation included significant behavioral disturbances and psychosis (hallucinations, disabling anxiety, aggressive behavior, and sleep disorder), leading to multiple therapeutic attempts. Intervention with benzodiazepines appeared most efficacious, resulting in decreased aggression and agitation and improvement in anxiety. A review of 56 published and unpublished studies of SSADH-deficient patients revealed that 42% manifested behavioral disturbances, whereas 13% (predominantly adults) displayed psychotic symptomatology. To explore the potential biochemical basis of these behavioral abnormalities, we studied cerebrospinal fluid derived from 13 patients, which revealed significantly elevated GHB (65- to 230-fold), high free and total GABA (up to threefold), and low glutamine. Although within the control range, homovanillic and 5-hydroxyindoleacetic acids (end products of dopamine and serotonin metabolism, respectively) showed a significant linear correlation with increasing GHB concentration, suggesting enhanced dopamine and serotonin turnover. We conclude that elevated GABA combined with low glutamine suggest disruption of the glial-neuronal glutamine/GABA/glutamate shuttle necessary for replenishment of neuronal neurotransmitters, whereas altered dopamine and serotonin metabolism may be causally linked to the hyperkinetic movement disorders and behavioral disturbances seen in SSADH-deficient patients.

Adult↗