Behavior of purified arginine desiminase from S. faecalis

Petrack, Barbara; Sullivan, Leanora; Ratner, S.

doi:10.1016/0003-9861(57)90485-x

Cited by 45 publications

(17 citation statements)

References 29 publications

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“…It was with this microorganism that both pathways were originally demonstrated (20,24,45,50), the corresponding enzymatic steps were characterized and shown to be coordinately induced by arginine or agmatine (48,49), the enzymes (except AgDI) were purified (31,32,42,56), and CK (the ADI pathway isozyme) was crystallized and its structure determined at atomic resolution (29,30). Despite the abundance of biochemical information, there was little genetic information on these routes in E. faecalis until we sequenced the genes and determined the gene structure, organization, and some regulatory features for the components of the ADI pathway (3).…”

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confidence: 99%

The Gene Cluster for Agmatine Catabolism ofEnterococcus faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing Its Reaction

et al. 2007

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Enterococcus faecalis makes ATP from agmatine in three steps catalyzed by agmatine deiminase (AgDI), putrescine transcarbamylase (PTC), and carbamate kinase (CK). An antiporter exchanges putrescine for agmatine. We have cloned the E. faecalis ef0732 and ef0734 genes of the reported gene cluster for agmatine catabolism, overexpressed them in Escherichia coli, purified the products, characterized them functionally as PTC and AgDI, and crystallized and X-ray diffracted them. The 1.65-Å-resolution structure of AgDI forming a covalent adduct with an agmatine-derived amidine reactional intermediate is described. We provide definitive identification of the gene cluster for agmatine catabolism and confirm that ornithine is a genuine but poor PTC substrate, suggesting that PTC (found here to be trimeric) evolved from ornithine transcarbamylase. N-(Phosphonoacetyl)-putrescine was prepared and shown to strongly (K i ‫؍‬ 10 nM) and selectively inhibit PTC and to improve PTC crystallization. We find that E. faecalis AgDI, which is committed to ATP generation, closely resembles the AgDIs involved in making polyamines, suggesting the recruitment of a polyamine-synthesizing AgDI into the AgDI pathway. The arginine deiminase (ADI) pathway of arginine catabolism probably supplied the genes for PTC and CK but not those for the agmatine/putrescine antiporter, and thus the AgDI and ADI pathways are not related by a single "en bloc" duplication event. The AgDI crystal structure reveals a tetramer with a five-blade propeller subunit fold, proves that AgDI closely resembles ADI despite a lack of sequence identity, and explains substrate affinity, selectivity, and Cys357-mediated-covalent catalysis. A three-tongued agmatine-triggered gating opens or blocks access to the active center.In addition to the fermentation of carbohydrates, Enterococcus faecalis (formerly Streptococcus faecalis) is able to use arginine and its decarboxylated derivative agmatine as energy sources for growth (8,10,45,48,49). Arginine and agmatine are metabolized via the arginine deiminase (ADI) and agmatine deiminase (AgDI) pathways, respectively. The two metabolic routes are very similar and include the sequential action of three enzymes (48, 49) and one antiporter (11), which are analogous in the two pathways. Arginine and agmatine are deiminated by ADI (EC 3.5.3.6) and AgDI (EC 3.5.3.12), respectively, yielding citrulline and carbamoyl putrescine, which are phosphorolyzed by ornithine transcarbamylase (OTC) (EC 2.1.3.3) and putrescine transcarbamylase (PTC) (EC 2.1.3.6). This generates carbamoyl phosphate for use in ADP phosphorylation by pathway-specific carbamate kinase (CK) (EC 2.7.2.2) isozymes, producing one ATP molecule (48, 49). The resulting ornithine and putrescine are exchanged with external arginine or agmatine by an arginine/ ornithine antiporter in one pathway and by an agmatine/putrescine antiporter in the other pathway (11).Possibly no microbial species has been more important for the biochemical characterization of the ADI and AgDI pathways tha...

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The Gene Cluster for Agmatine Catabolism ofEnterococcus faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing Its Reaction

et al. 2007

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“…The ADI pathway was originally demonstrated and characterized in this microorganism (22,25,62), and its enzymes were purified (40,41,50) and shown to be coordinately induced by arginine (61). Recently the first three-dimensional structure of a CK was determined (38) on the enzyme isolated from what was believed to be Enterococcus faecium (6) but that we presently show to be E. faecalis (called here E. faecalis SD10).…”

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Gene Structure, Organization, Expression, and Potential Regulatory Mechanisms of Arginine Catabolism inEnterococcus faecalis

2002

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Although Enteroccus faecalis is the paradigm for biochemical studies on the arginine deiminase (ADI) pathway of fermentative arginine catabolism, little genetic information exists on this pathway in this organism. We fill this important gap by characterizing, in an 8,228-bp region cloned from a gt11 genomic library of E. faecalis, a five-gene cluster forming a transcriptional unit (revealed by Northern blots and primer extension in E. faecalis) that corresponds to the ADI operon. Four additional genes in the opposite DNA strand and one in the same DNA strand are also identified. Studies on the protein products, including heterologous expression and/or sequence comparisons, allow us to ascertain or propose functions for all but 1 of the 10 genes. The ADI operon genes, arcABCRD, encode, respectively, ADI, ornithine transcarbamylase, carbamate kinase, a putative Crp/Fnr-type regulator (ArcR), and a putative ornithine-arginine antiporter (ArcD). Arginine induces the expression of arcABCRD, most likely by means of two homologous ArgR/AhrC-type regulators encoded by two genes, argR1 and argR2, that precede arcABCRD in each DNA strand and that are transcribed monocistronically, their transcription being influenced differentially by glucose and arginine. Potential ArgR1/ArgR2 (double and single) binding sequences are found in the promoter regions of arcA and of argR1/argR2 themselves. In addition, putative binding sequences for ArcR and for CcpA are found, respectively, in the argR1/ argR2 and arcA promoter regions. Of the three other genes identified, two form a transcriptional unit and encode a putative metal-sensitive transcriptional regulator (ArsR) and a cysteine protease.A number of microorganisms generate ATP fermentatively from arginine by a route (1) (Fig. 1) in which arginine is deiminated by arginine deiminase (ADI; EC 3.5.3.6), the resulting citrulline is phosphorolyzed by ornithine transcarbamylase (OTC; EC 2.1.3.3), giving ornithine and carbamoyl phosphate, and finally the carbamoyl phosphate is used to phosphorylate ADP in a reaction catalyzed by carbamate kinase (CK; EC 2.7.2.2), yielding ATP. This route, called the ADI pathway, operates in many eubacteria (1,10,12,64) and in some archaea (53) and unicellular eukaryotes (59, 71), but it has not been found in multicellular organisms.Possibly no microbial species has been more important for the biochemical characterization of the ADI pathway than Enterococcus faecalis (formerly Streptococcus faecalis). The ADI pathway was originally demonstrated and characterized in this microorganism (22,25,62), and its enzymes were purified (40, 41, 50) and shown to be coordinately induced by arginine (61). Recently the first three-dimensional structure of a CK was determined (38) on the enzyme isolated from what was believed to be Enterococcus faecium (6) but that we presently show to be E. faecalis (called here E. faecalis SD10).Despite the abundant information derived from E. faecalis on the biochemistry of the ADI pathway, there was no other genetic information about...

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“…The properties of argininosuccinate synthetase were initially delineated from protein obtained from bovine liver (3,4). Argininosuccinate synthetase has since been studied extensively at both the protein and genetic levels, and reviews are available (5,6).…”

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Molecular definition of bovine argininosuccinate synthetase deficiency.

Dennis

Healy

Beaudet

et al. 1989

Proc. Natl. Acad. Sci. U.S.A.

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Citrullinemia is an inborn error of metabolism due to deficiency of the urea cycle enzyme, argininosuccinate synthetase [L-citrulline:L-aspartate ligase (AMP-forming), EC 6.3.4.5]. The disease was first described in humans but was recently reported in dairy cattle in Australia. Here we report the nucleotide sequence of the normal bovine cDNA for argininosuccinate synthetase and the mutation present in animals with citrullinemia. Analysis of DNA from affected animals by Southern blotting did not readily identify the mutation in the bovine gene. RNA (Northern) blotting revealed a major reduction in the steady-state amount of mRNA in the liver of affected animals to <5% of controls. The bovine cDNA was cloned and sequenced and revealed 96% identity with the deduced human sequence at the amino acid level. Starting with mutant bovine liver, the mRNA was reverse-transcribed; the cDNA product was amplified with the polymerase chain reaction, cloned, and sequenced. The sequence revealed a C -+ T transition converting arginine-86 (CGA) to a nonsense codon (TGA). A second C --T transition represented a polymorphism in proline-175 (CCC --> CCT). The mutation and the polymorphism were confirmed by amplification of genomic DNA and demonstration with restriction endonuclease enzymes of both the loss of an Ava II site in DNA from mutant animals at codon 86 and the presence or absence of a Dde I site at codon 175. The loss of the Ava II site can be used for rapid, economical, nonradioactive detection of heterozygotes for bovine citrullinemia.

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Behavior of purified arginine desiminase from S. faecalis

Cited by 45 publications

References 29 publications

The Gene Cluster for Agmatine Catabolism ofEnterococcus faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing Its Reaction

The Gene Cluster for Agmatine Catabolism ofEnterococcus faecalis: Study of Recombinant Putrescine Transcarbamylase and Agmatine Deiminase and a Snapshot of Agmatine Deiminase Catalyzing Its Reaction

Gene Structure, Organization, Expression, and Potential Regulatory Mechanisms of Arginine Catabolism inEnterococcus faecalis

Molecular definition of bovine argininosuccinate synthetase deficiency.

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