Purification and characterization of a novel enzyme, N-carbamoylsarcosine amidohydrolase, from Pseudomonas putida 77

Novel Metabolic Pathway for N-Methylpyrrolidone Degradation in Alicycliphilus sp. Strain BQ1

The molecular mechanisms underlying the biodegradation of N-methylpyrrolidone (NMP), a widely used industrial solvent that produces skin irritation in humans and is teratogenic in rats, are unknown. Alicycliphilus sp. strain BQ1 degrades NMP. By studying a transposon-tagged mutant unable to degrade NMP, we identified a six-gene cluster (nmpABCDEF) that is transcribed as a polycistronic mRNA and encodes enzymes involved in NMP biodegradation. nmpA and the transposon-affected gene nmpB encode an N-methylhydantoin amidohydrolase that transforms NMP to γ-N-methylaminobutyric acid; this is metabolized by an amino acid oxidase (NMPC), either by demethylation to produce γ-aminobutyric acid (GABA) or by deamination to produce succinate semialdehyde (SSA). If GABA is produced, the activity of a GABA aminotransferase (GABA-AT), not encoded in the nmp gene cluster, is needed to generate SSA. SSA is transformed by a succinate semialdehyde dehydrogenase (SSDH) (NMPF) to succinate, which enters the Krebs cycle. The abilities to consume NMP and to utilize it for growth were complemented in the transposon-tagged mutant by use of the nmpABCD genes. Similarly, Escherichia coli MG1655, which has two SSDHs but is unable to grow in NMP, acquired these abilities after functional complementation with these genes. In wild-type (wt) BQ1 cells growing in NMP, GABA was not detected, but SSA was present at double the amount found in cells growing in Luria-Bertani medium (LB), suggesting that GABA is not an intermediate in this pathway. Moreover, E. coli GABA-AT deletion mutants complemented with nmpABCD genes retained the ability to grow in NMP, supporting the possibility that γ-N-methylaminobutyric acid is deaminated to SSA instead of being demethylated to GABA.IMPORTANCEN-Methylpyrrolidone is a cyclic amide reported to be biodegradable. However, the metabolic pathway and enzymatic activities for degrading NMP are unknown. By developing molecular biology techniques for Alicycliphilus sp. strain BQ1, an environmental bacterium able to grow in NMP, we identified a six-gene cluster encoding enzymatic activities involved in NMP degradation. These findings set the basis for the study of new enzymatic activities and for the development of biotechnological processes with potential applications in bioremediation.

The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems

The Rut pathway is composed of seven proteins, all of which are required by Escherichia coli K-12 to grow on uracil as the sole nitrogen source. The RutA and RutB proteins are central: no spontaneous suppressors arise in strains lacking them. RutA works in conjunction with a flavin reductase (RutF or a substitute) to catalyze a novel reaction. It directly cleaves the uracil ring between N-3 and C-4 to yield ureidoacrylate, as established by both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry. Although ureidoacrylate appears to arise by hydrolysis, the requirements for the reaction and the incorporation of (18)O at C-4 from molecular oxygen indicate otherwise. Mass spectrometry revealed the presence of a small amount of product with the mass of ureidoacrylate peracid in reaction mixtures, and we infer that this is the direct product of RutA. In vitro RutB cleaves ureidoacrylate hydrolytically to release 2 mol of ammonium, malonic semialdehyde, and carbon dioxide. Presumably the direct products are aminoacrylate and carbamate, both of which hydrolyze spontaneously. Together with bioinformatic predictions and published crystal structures, genetic and physiological studies allow us to predict functions for RutC, -D, and -E. In vivo we postulate that RutB hydrolyzes the peracid of ureidoacrylate to yield the peracid of aminoacrylate. We speculate that RutC reduces aminoacrylate peracid to aminoacrylate and RutD increases the rate of spontaneous hydrolysis of aminoacrylate. The function of RutE appears to be the same as that of YdfG, which reduces malonic semialdehyde to 3-hydroxypropionic acid. RutG appears to be a uracil transporter.

Crystal structure of the yeast nicotinamidase Pnc1p

The yeast nicotinamidase Pnc1p acts in transcriptional silencing by reducing levels of nicotinamide, an inhibitor of the histone deacetylase Sir2p. The Pnc1p structure was determined at 2.9A resolution using MAD and MIRAS phasing methods after inadvertent crystallization during the pursuit of the structure of histidine-tagged yeast isocitrate dehydrogenase (IDH). Pnc1p displays a cluster of surface histidine residues likely responsible for its co-fractionation with IDH from Ni(2+)-coupled chromatography resins. Researchers expressing histidine-tagged proteins in yeast should be aware of the propensity of Pnc1p to crystallize, even when overwhelmed in concentration by the protein of interest. The protein assembles into extended helical arrays interwoven to form an unusually robust, yet porous superstructure. Comparison of the Pnc1p structure with those of three homologous bacterial proteins reveals a common core fold punctuated by amino acid insertions unique to each protein. These insertions mediate the self-interactions that define the distinct higher order oligomeric states attained by these molecules. Pnc1p also acts on pyrazinamide, a substrate analog converted by the nicotinamidase from Mycobacterium tuberculosis into a product toxic to that organism. However, we find no evidence for detrimental effects of the drug on yeast cell growth.

[Structural and functional analysis of enzymes and their application to clinical analysis--study on Pseudomonas putida formaldehyde dehydrogenase]

Formaldehyde dehydrogenase (PFDH) was isolated from the creatinine-decomposing bacterium Pseudomonas putida, and its gene has been cloned. PFDH is unique because it was the only enzyme that catalyzed the dehydrogenation of formaldehyde without glutathione. PFDH belongs to a zinc-containing alcohol dehydrogenase family. Quantitative analysis of the reaction products using NMR revealed that the enzyme is not simply a dehydrogenase but is an aldehyde dismutase catalyzing a simultaneous conversion of both aldehyde to carboxylate and aldehyde to alcohol. The enzyme contains a tightly bound cofactor of NAD+/NADH per subunit and is classified as a nicotinoprotein. The enzyme reaction can proceed without external addition of the nucleotide cofactor. The formaldehyde was crystallized using the hanging-drop vapor diffusion method with ammonium sulfate as a precipitant. The crystal structure was determined using the multiwavelength anomalous diffraction method with intrinsic zinc ions. The overall structure of PFDH is similar to that of a classic horse liver alcohol dehydrogenase. However, a comparison of these structures indicated that the insertion loop specifically found in PFDH may be responsible for the tight binding of the cofactor, thereby making PFDH a dismutase.

Creatine and creatinine metabolism

The goal of this review is to present a comprehensive survey of the many intriguing facets of creatine (Cr) and creatinine metabolism, encompassing the pathways and regulation of Cr biosynthesis and degradation, species and tissue distribution of the enzymes and metabolites involved, and of the inherent implications for physiology and human pathology. Very recently, a series of new discoveries have been made that are bound to have distinguished implications for bioenergetics, physiology, human pathology, and clinical diagnosis and that suggest that deregulation of the creatine kinase (CK) system is associated with a variety of diseases. Disturbances of the CK system have been observed in muscle, brain, cardiac, and renal diseases as well as in cancer. On the other hand, Cr and Cr analogs such as cyclocreatine were found to have antitumor, antiviral, and antidiabetic effects and to protect tissues from hypoxic, ischemic, neurodegenerative, or muscle damage. Oral Cr ingestion is used in sports as an ergogenic aid, and some data suggest that Cr and creatinine may be precursors of food mutagens and uremic toxins. These findings are discussed in depth, the interrelationships are outlined, and all is put into a broader context to provide a more detailed understanding of the biological functions of Cr and of the CK system.

Screening of novel microbial enzymes for the production of biologically and chemically useful compounds

Enzymes have been generally accepted as superior catalysts in organic synthesis. Micro-organisms in particular have been regarded as treasure sources of useful enzymes. The synthetic technology using microbial enzymes or micro-organisms themselves is called microbial transformation. In designing a microbial transformation process, one of the most important points is to find a suitable enzyme for the reaction of interest. Various kinds of novel enzymes for specific transformations have been discovered in micro-organisms and their potential characteristics revealed. This article reviews our current results on the discovery of novel enzymes for the production of biologically and chemically useful compounds, and emphasizes the importance of screening enzymes in a diverse microbial world.

Purification and characterization of N-carbamoyl-L-amino acid amidohydrolase with broad substrate specificity from Alcaligenes xylosoxidans

N-Carbamoyl-L-amino acid amidohydrolase was purified to homogeneity for the first time from Alcaligenes xylosoxidans. The enzyme showed high affinity toward N-carbamoyl-L-amino acids with long-chain aliphatic or aromatic substituents, and hydrolyzed those with short-chain substituents quite well. The enzyme hydrolyzed N-formyl- and N-acetylamino acids quickly and very slowly, respectively. The enzyme did not hydrolyze beta-ureidopropionate and ureidosuccinate. The relative molecular mass of the native enzyme was about 135,000 and the enzyme consisted of two identical polypeptide chains. The enzyme activity was significantly inhibited by sulfhydryl reagents and required the following divalent metal ions: Mn2+, Ni2+ and Co2+.

Purification and characterization of an ATP-dependent amidohydrolase, N-methylhydantoin amidohydrolase, from Pseudomonas putida 77

N-Methylhydantoin amidohydrolase, an ATP-dependent amidohydrolase involved in microbial degradation of creatinine, was purified 70-fold to homogeneity, with a 62% overall recovery, and was crystallized from Pseudomonas putida 77. The enzyme has a relative molecular mass of 300,000. It is a tetramer of two identical small subunits (M(r) 70,000) and two identical large subunits (M(r) 80,000). The enzyme requires ATP for the amidohydrolysis of N-methylhydantoin and vice versa. Mg2+, Mn2+ or Co2+, and K+, NH4+, Rb+ or Cs+, were absolutely required concomitantly for the enzyme activity as divalent and monovalent cations, respectively. The Km and Vmax values for N-methylhydantoin were 32 microM and 9.0 mumol.min-1.mg protein-1. The hydrolysis of amide compounds and coupled hydrolysis of ATP were observed with hydantoin, DL-5-methylhydantoin, glutarimide and succimide in addition to N-methylhydantoin. 2-Pyrrolidone, 2-oxazolidone, delta-valerolactam, 2,4-thiazolidinedione, 2-imidazolidone, D-5-oxoproline methyl ester, DL-5-oxoproline methyl ester, and naturally occurring pyrimidine compounds, i.e. dihydrouracil, dihydrothymine, uracil, and thymine, effectively stimulated ATP hydrolysis by the enzyme without undergoing detectable self-hydrolysis.

Thermostable N-carbamoyl-D-amino acid amidohydrolase: screening, purification and characterization

A thermostable N-carbamoyl-D-amino acid amidohydrolase was found in the cells of newly isolated bacterium. Blastobacter sp. A17p-4. The bacterium also showed D-specific hydantoinase activity. The N-carbamoyl-D-amino acid amidohydrolase activity of the cells exhibited a temperature optimum at 50-55 degrees C, and was stable up to 50 degrees C. The N-carbamoyl-D-amino acid amidohydrolase of Blastobacter sp. A17p-4 was purified to homogeneity and characterized. It has a relative molecular weight of about 120,000 and consists of three identical subunits with a relative molecular weight of about 40,000. N-Carbamoyl-D-amino acids having hydrophobic groups served as good substrates for the enzyme. It has been suggested that D-amino acid production from DL-5-substituted hydantoin involves the action of a series of enzymes involved in pyrimidine degradation, namely amide-ring opening enzyme, dihydropyrimidinase, and N-carbamoylamide hydrolyzing enzyme, beta-ureidopropionase. However, the purified enzyme did not hydrolyze beta-ureidopropionate; suggesting that the N-carbamoyl-D-amino acid amidohydrolase coexisting with D-specific hydantoinase, probably dihydropyrimidinase, in Blastobacter sp. A17p-4 is different from beta-ureidopropionase.

Beta-ureidopropionase with N-carbamoyl-alpha-L-amino acid amidohydrolase activity from an aerobic bacterium, Pseudomonas putida IFO 12996

beta-Ureidopropionase of aerobic bacterial origin was purified to homogeneity from Pseudomonas putida IFO 12996. The enzyme shows a broad substrate specificity. In addition to beta-ureidopropionate (Km 3.74 mM, Vmax 4.12 U/mg), gamma-ureido-n-butyrate (Km 11.6 mM, Vmax 19.4 U/mg), and several N-carbamoyl-alpha-amino acids, such as N-carbamoylglycine (Km 0.68 mM, Vmax 9.14 x 10(-2) U/mg), N-carbamoyl-L-alanine (Km 1.56 mM, Vmax 1.00 U/mg), N-carbamoyl-L-serine (Km 75.1 mM, Vmax 3.78 U/mg), and N-carbamoyl-DL-alpha-amino-n-butyrate (Km 2.81 mM, Vmax 1.08 U/mg), are also hydrolyzed. The hydrolysis of N-carbamoyl-alpha-amino acids is strictly L enantiomer specific. N-Formyl-L-alanine and N-acetyl-L-alanine are also hydrolyzed by the enzyme, but the rate of hydrolysis is lower than the rate for N-carbamoyl-L-alanine. The enzyme requires a divalent metal ion, such as Co2+, Ni2+ or Mn2+, for activity, and is significantly affected by sulfhydryl reagents. The enzyme consists of two polypeptide chains with identical relative molecular mass M(r) 45000. The broad substrate specificity and metal ion dependence of the enzyme show that the beta-ureidopropionase of this aerobic bacterium is quite different from the beta-ureidopropionases of mammals and anaerobic bacteria.

N-carbamoyl-D-amino acid amidohydrolase from Comamonas sp. E222c purification and characterization

N-Carbamoyl-D-amino acid amidohydrolase was purified 119-fold, with 36% overall recovery from a cell-free extract of Comamonas sp. E222c. The purified enzyme was homogeneous as judged by SDS/PAGE. The relative molecular mass of the native enzyme was 120,000 and that of the subunit was 40,000. The purified enzyme hydrolyzed various N-carbamoyl-D-amino acids to D-amino acids, ammonia and carbon dioxide. N-Carbamoyl-D-amino acids having hydrophobic groups served as good substrates for the enzyme. The Km and Vmax values for N-carbamoyl-D-phenylalanine were 19.7 mM and 13.1 units/mg, respectively, and those for N-carbamoyl-D-p-hydroxyphenylglycine were 13.1 mM and 0.56 units/mg, respectively. The enzyme strictly recognized the configuration of the substrate and only the D-enantiomer of the N-carbamoyl amino acid was hydrolyzed. The enzyme activity was not significantly affected by N-carbamoyl-L-amino acids and ammonia. The enzyme was sensitive to thiol reagents and did not require metal ions for its activity. The enzyme did not hydrolyze N-carbamoyl-beta-alanine or N-carbamoyl-DL-aspartate suggesting that the enzyme is different from the N-carbamoylamide-hydrolyzing enzymes involved in the pyrimidine degradation pathway. The enzyme did not hydrolyze allantoin and allantoic acid, which are intermediates in purine degradation, N-carbamoylsarcosine and citrulline, suggesting that it is a novel N-carbamoylamide amidohydrolase.

Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2.0 A resolution

N-carbamoylsarcosine amidohydrolase from Arthrobacter sp., a tetramer of polypeptides with 264 amino acid residues each, has been crystallized and its structure solved and refined at 2.0 A resolution, to a crystallographic R-factor of 18.6%. The crystals employed in the analysis contain one tetramer of 116,000 M(r) in the asymmetric unit. The structure determination proceeded by multiple isomorphous replacement, followed by solvent-flattening and density averaging about the local diads within the tetramer. In the final refined model, the root-mean-square deviation from ideality is 0.01 A for bond distances and 2.7 degrees for bond angles. The asymmetric unit consists of 7853 protein atoms, 431 water molecules and four sulfate ions bound into the putative active site clefts in each subunit. One subunit contains a central six-stranded parallel beta-pleated sheet packed by helices on both sides. On one side, two helices face the solvent, while two of the helices on the other side are buried in the tight intersubunit contacts. The catalytic center of the enzyme, tentatively identified by inhibitor binding, is located at the interface between two subunits and involves residues from both. It is suggested that the nucleophilic group involved in hydrolysis of the substrate is the thiol group of Cys117 and a nucleophilic addition-elimination mechanism is proposed.

Creatinine and N-methylhydantoin degradation in two newly isolated Clostridium species

With N-methylhydantoin (NMH) as the main organic substrate, two strictly anaerobic spore forming Gram-positive bacterial strains were isolated from sewage sludge. These strains, named Clostridium sp. FS23 and Clostridium sp. FS41, totally degraded NMH, via N-carbamoylsarcosine (CS) and sarcosine as intermediates. Strain FS23 grew also with creatinine, which was converted to NMH by creatinine iminohydrolase (EC 3.5.4.21). This enzyme was formed at high rates with all substrates tested. Cytosine and 5-fluorocytosine were not utilized as substrates by creatinine iminohydrolase preparations purified to a homogeneity of 98%. NMH amidohydrolase (NMHase) and N-carbamoylsarcosine amidohydrolase (CSHase) turned out to be inducible in both strains. Other than in aerobic organisms, NMHase from these two isolated did not require ATP for enzymatic activity. SH-group protecting agents were not necessary for stability.

Microbial enzymes for creatinine assay: a review

A novel metabolic pathway for the degradation of creatinine with N-methylhydantoin, N-carbamoylsarcosine and sarcosine as successive intermediates was found to operate in Pseudomonas putida 77 and many other microorganisms. Enzymes involved in this pathway were purified from cells of P. putida 77 and characterized. The first step, deimination of creatinine, is catalyzed by cytosine deaminase/creatinine deiminase. The following two steps, ring-opening of N-methylhydantoin and decarbamoylation of N-carbamoylsarcosine, are catalyzed by new enzymes, N-methylhydantoin amidohydrolase and N-carbamoylsarcosine amidohydrolase, respectively. The former requires ATP, Mg2+, and K+ for the hydrolysis and the reaction proceeds as follows: N-methylhydantoin + ATP + 2 H2O----N-carbamoylsarcosine + ADP + Pi. The latter catalyzes the following reaction; N-carbamoylsarcosine + H2O----sarcosine + NH3 + CO2. Sarcosine dehydrogenase was found to be the responsible enzyme for the oxidation of sarcosine to glycine in P. putida 77, but sarcosine oxidase was also found to be involved in this oxidation in several microorganisms. These enzymes were found to be useful tools for determination of creatinine.

Amidohydrolysis of N-methylhydantoin coupled with ATP hydrolysis

A new enzyme, N-methylhydantoin amidohydrolase, was highly purified from Pseudomonas putida 77: it catalyzes the hydrolysis of N-methylhydantoin to N-carbamoylsarcosine with the concomitant stoichiometric cleavage of ATP to ADP and orthophosphate. The enzyme absolutely requires ATP, MG2+ and K+ for the N-methylhydantoin hydrolysis. The rapid and complete degradation of N-methylhydantoin during the cultivation of P. putida 77, which rapidly degrades creatinine via only N-methylhydantoin and which shows high activities of the enzymes involved in creatinine degradation (Yamada et al. (1985) FEMS Microbiol. Lett. 30, 337-340), seems to be due to the continuous ATP-generation during cultivation.