Structure and mechanism of tryptophan indole-lyase and tyrosine phenol-lyase

Phillips, Robert S.; Demidkina, Tatyana V.; Faleev, N. G.

doi:10.1016/s1570-9639(03)00089-x

Cited by 41 publications

(29 citation statements)

References 26 publications

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“…Phenol, which is a precursor of PhS, is metabolized from tyrosine by tyrosine phenol-lyase (KEGG: K01668). Both tryptophanase and tyrosine phenol-lyase were classified as pyridoxal 5'-phosphate-dependent enzymes that catalyze the β-elimination reaction, and have the same motif sequence [21]. We assigned all OTUs to the reference genome database, and listed the OTUs containing the tryptophanase/tyrosine phenol-lyase gene (K01667/K01668) in the genome sequence in table 3.…”

Section: Resultsmentioning

confidence: 99%

Uremic Toxin-Producing Gut Microbiota in Rats with Chronic Kidney Disease

Kikuchi

Ueno

Itoh

et al. 2016

Nephron

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Background: In patients with chronic kidney disease (CKD), many metabolites of gut microbiota retain in the body as uremic toxins (UTs). However, the kinds of bacteria producing UTs are rarely discussed. Methods: We analyzed UT production and the composition of gut microbiota in CKD rats and cecectomized rats. AST-120, a spherical carbon adsorbent, was administrated to evaluate how the precursors of UT affect gut microbiota. Serum and urine levels of UTs were quantified by liquid chromatography/electrospray ionization-tandem mass spectrometry. Gut microbiota were analyzed using 454-pyrosequencing of the 16S rRNA gene. Operational taxonomic unit (OTU) clustering and UniFrac analysis were performed to compare gut microbiota among the groups. Results: Serum and urine levels of indoxyl sulfate and phenyl sulfate were higher in CKD versus control rats (p < 0.05). AST-120 administration decreased UT production (p < 0.01) and changed overall gut microbiota composition in CKD rats. UT urinary excretion and gut microbiota composition changed in cecectomized rats, with the relative abundance of Clostridia- and Bacteroidia-affiliated species being significantly reduced (p < 0.01). We identified candidate indole- and phenol-producing intestinal microbiota, 3 Clostridia, and 2 Bacteroidia. These OTUs have a tryptophanase/tyrosine phenol-lyase gene in the closest sequenced genome out of the OTUs declined following cecectomy. Conclusion: Our data suggest that UT production is correlated with a subset of indigenous gut microbiota. However, UT may be induced by other non-symbiotic microbiota that are influenced by factors other than microbiota populations. The relationship between specific microbiota and UTs in patients requires further clarification.

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Section: Resultsmentioning

confidence: 99%

Uremic Toxin-Producing Gut Microbiota in Rats with Chronic Kidney Disease

Kikuchi

Ueno

Itoh

et al. 2016

Nephron

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“…In bacteria and other organisms, there are multiple PLP-dependent enzymes known to generate 2-AA as part of the biochemical mechanisms, including serine/threonine dehydratases (30,33), cysteine desulfhydrases (34), tryptophanase (35), and tryptophan synthase (36), among others. While the reactivity of aminoacrylate has been emphasized by studies in vitro, the potential for this and similar enamines to cause significant damage in vivo has only recently come to light based on work with RidA (2, 9, 10).…”

Section: Resultsmentioning

confidence: 99%

In the Absence of RidA, Endogenous 2-Aminoacrylate Inactivates Alanine Racemases by Modifying the Pyridoxal 5′-Phosphate Cofactor

Flynn

Downs

2013

J Bacteriol

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Members of the RidA (YjgF/YER057c/UK114) protein family are broadly conserved across the domains of life. In vitro, these proteins deaminate 3-or 4-carbon enamines that are generated as mechanistic intermediates of pyridoxal 5=-phosphate (PLP)-dependent serine/threonine dehydratases. The three-carbon enamine 2-aminoacrylate can inactivate some enzymes by forming a covalent adduct via a mechanism that has been well characterized in vitro. The biochemical activity of RidA suggested that the phenotypes of ridA mutant strains were caused by the accumulation of reactive enamine metabolites. The data herein show that in ridA mutant strains of Salmonella enterica, a stable 2-aminoacrylate (2-AA)/PLP adduct forms on the biosynthetic alanine racemase, Alr, indicating the presence of 2-aminoacrylate in vivo. This study confirms the deleterious effect of 2-aminoacrylate generated by metabolic enzymes and emphasizes the need for RidA to quench this reactive metabolite.

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“…82 and 83 and references therein), tryptophan indole-lyase and tyrosine phenol-lyase (see Ref. 84 and references therein) has been determined from pre-steady-state studies. For the first three enzymes, the catalytic reaction is composed by two distinct half-reactions as follows: the ␤-elimination is followed by a ␤-addition where nucleophilic agents, indole, sulfide, and homocysteine, respectively, react with the ␣-aminoacrylate Schiff base to form the final product, L-tryptophan, L-cysteine, and L-cystathionine, respectively.…”

Section: Cystine Cysteinementioning

confidence: 99%

Sulfur Mobilization in Cyanobacteria

Campanini

Schiaretti

Abbruzzetti

et al. 2006

Journal of Biological Chemistry

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Sulfur mobilization represents one of the key steps in ubiquitous Fe-S clusters assembly and is performed by a recently characterized set of proteins encompassing cysteine desulfurases, assembly factors, and shuttle proteins. Despite the evolutionary conservation of these proteins, some degree of variability among organisms was observed, which might reflect functional specialization. L-Cyst(e)ine lyase (C-DES), a pyridoxal 5-phosphatedependent enzyme identified in the cyanobacterium Synechocystis, was reported to use preferentially cystine over cysteine with production of cysteine persulfide, pyruvate, and ammonia. In this study, we demonstrate that C-DES sequences are present in all cyanobacterial genomes and constitute a new family of sulfur-mobilizing enzymes, distinct from cysteine desulfurases. The functional properties of C-DES from Synechocystis sp. PCC 6714 were investigated under pre-steady-state and steady-state conditions. Single wavelength and rapid scanning stopped-flow kinetic data indicate that the internal aldimine reacts with cystine forming an external aldimine that rapidly decays to a transient quinonoid species and stable tautomers of the ␣-aminoacrylate Schiff base. In the presence of cysteine, the transient formation of a dipolar species precedes the selective and stable accumulation of the enolimine tautomer of the external aldimine, with no formation of the ␣-aminoacrylate Schiff base under reducing conditions. Effective sulfur mobilization from cystine might represent a mechanism that allows adaptation of cyanobacteria to different environmental conditions and to light-dark cycles.

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Structure and mechanism of tryptophan indole-lyase and tyrosine phenol-lyase

Cited by 41 publications

References 26 publications

Uremic Toxin-Producing Gut Microbiota in Rats with Chronic Kidney Disease

Uremic Toxin-Producing Gut Microbiota in Rats with Chronic Kidney Disease

In the Absence of RidA, Endogenous 2-Aminoacrylate Inactivates Alanine Racemases by Modifying the Pyridoxal 5′-Phosphate Cofactor

Sulfur Mobilization in Cyanobacteria

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