Study of the amidase signature group

Chebrou, H.; Bigey, Frédéric; Arnaud, A.; Galzy, P.

doi:10.1016/s0167-4838(96)00145-8

Cited by 129 publications

(112 citation statements)

References 38 publications

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“…With GatA, approximately 150 amino acids of the alignment is comprised of the Gly/Ser rich amidase signature sequence which is highly conserved within the greater amidase family. 45 In order to resolve the divergence of archaeal and bacterial GatCAB, we examined a phylogeny based on concatenation of GatA and GatB sequence (Fig. 6).…”

Section: Gatab Divides Into Bacterial and Archaeal Typesmentioning

confidence: 99%

On the Evolution of the tRNA-Dependent Amidotransferases, GatCAB and GatDE

Sheppard

Söll

2008

Journal of Molecular Biology

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SummaryGlutaminyl-tRNA synthetase and asparaginyl-tRNA synthetase evolved from glutamyl-tRNA synthetase and aspartyl-tRNA synthetase, respectively, after the split in the last universal communal ancestor (LUCA). Glutaminyl-tRNA Gln and asparaginyl-tRNA Asn were likely formed in LUCA by amidation of the mischarged species, glutamyl-tRNA Gln and aspartyl-tRNA Asn , by tRNA-dependent amidotransferases as is still the case in most bacteria and all known archaea. The amidotransferase GatCAB is found in both domains of life while the heterodimeric amidotransferase, GatDE, is found only in Archaea. The GatB and GatE subunits belong to a unique protein family with Pet112 that is encoded in the nuclear genomes of numerous eukaryotes. GatE was thought to have evolved from GatB after the emergence of the modern lines of decent. Our phylogenetic analysis though places the split between GatE and GatB prior to the phylogenetic divide between Bacteria and Archaea and Pet112 to be of mitochondrial origin. In addition, GatD appears to have emerged prior to the bacterialarchaeal phylogenetic divide. Thus, while GatDE is an archaeal signature protein it likely was present in LUCA together with GatCAB. Archaea retained both amidotransferases while Bacteria emerged with only GatCAB. The presence of GatDE has favored a unique archaeal tRNA Gln that may be preventing acquisition of glutaminyl-tRNA synthetase in Archaea. Archaeal GatCAB on the other hand has not favored a distinct tRNA Asn suggesting tRNA Asn recognition is not a major barrier to the retention of asparaginyl-tRNA synthetase in more Archaea.

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Section: Gatab Divides Into Bacterial and Archaeal Typesmentioning

confidence: 99%

On the Evolution of the tRNA-Dependent Amidotransferases, GatCAB and GatDE

Sheppard

Söll

2008

Journal of Molecular Biology

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“…A, full-length alignment of Arabidopsis amino acid sequence (GenBank TM accession number AY308736) with rat FAAH (GenBank TM accession number U72497) (28). These proteins are members of the AS sequence-containing superfamily that includes amidase or amidohydrolase (EC 3.5) enzymes involved in the reduction of organic nitrogen compounds and ammonia production (31,33). The AS region is underlined and consists of about 125 amino acids.…”

Section: X(ga)x(de)x(ga)xs(livm)rxp(gsac)mentioning

confidence: 99%

Molecular Identification of a Functional Homologue of the Mammalian Fatty Acid Amide Hydrolase in Arabidopsis thaliana

Shrestha

Dixon

Chapman

2003

Journal of Biological Chemistry

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N-Acylethanolamines (NAEs) are endogenous constituents of plant and animal tissues, and in vertebrates their hydrolysis terminates their participation as lipid mediators in the endocannabinoid signaling system. The membrane-bound enzyme responsible for NAE hydrolysis in mammals has been identified at the molecular level (designated fatty acid amide hydrolase, FAAH), and although an analogous enzyme activity was identified in microsomes of cotton seedlings, no molecular information is available for this enzyme in plants. Here we report the identification, the heterologous expression (in Escherichia coli), and the biochemical characterization of an Arabidopsis thaliana FAAH homologue. Candidate Arabidopsis DNA sequences containing a characteristic amidase signature sequence (PS00571) were identified in plant genome data bases, and a cDNA was isolated by reverse transcriptase-PCR using Arabidopsis genome sequences to develop appropriate oligonucleotide primers. The cDNA was sequenced and predicted to encode a protein of 607 amino acids with 37% identity to rat FAAH within the amidase signature domain (18% over the entire length). Residues determined to be important for FAAH catalysis were conserved between the Arabidopsis and rat protein sequences. In addition, a single transmembrane domain near the N terminus was predicted in the Arabidopsis protein sequence, similar to that of the rat FAAH protein. The putative plant FAAH cDNA was expressed as an epitope/ His-tagged fusion protein in E. coli and solubilized from cell lysates in the nonionic detergent, dodecyl maltoside. Affinity-purified recombinant protein was indeed active in hydrolyzing a variety of naturally occurring N-acylethanolamine types. Kinetic parameters and inhibition data for the recombinant Arabidopsis protein were consistent with these properties of the enzyme activity characterized previously in plant and animal systems. Collectively these data now provide support at the molecular level for a conserved mechanism between plants and animals for the metabolism of NAEs.N-Acylethanolamines (NAEs) 1 are lipid mediators that are produced from the phospholipase D-mediated hydrolysis of Nacylphosphatidylethanolamines, a minor membrane lipid constituent of cellular membranes (1). In animal systems, anandamide (NAE 20:4) acts as an endogenous ligand for cannabinoid receptors and has varied physiological roles, such as the modulation of neurotransmission in the central nervous system (2). Anandamide also activates vanilloid receptors, functions as an endogenous analgesic (3), and appears to be involved in neuroprotection (4,5). In other tissues, NAEs have been implicated in immunomodulation (6), synchronization of embryo development (7), and induction of apoptosis (8). These endogenous bioactive molecules lose their signaling activity upon hydrolysis by fatty acid amide hydrolase (FAAH; see Ref. 9).In plants NAEs are present in substantial amounts in desiccated seeds (ϳ1 g g Ϫ1 fresh weight), and their levels decline after a few hours of imbibition (10). Ind...

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“…A number of studies of amidase classification (Chebrou et al 1996;Fournand and Arnaud 2001) have shown that amidases fall into two categories. The first group, those belonging to the nitrilase superfamily, includes aliphatic amidases, which hydrolyze only short-chain aliphatic amides.…”

Section: Introductionmentioning

confidence: 99%

“…This second group includes aliphatic amidases which hydrolyze mid-length amides, some arylamides, α-aminoamides, and α-hydroxyamides. These enzymes often demonstrate enantioselectivity, and they belong to the group of the GGSS signature-containing amidase family (Chebrou et al 1996). Kobayashi et al (1997) have reported that these enzymes contain asparagine and serine residues in their active site.…”

Section: Introductionmentioning

confidence: 99%

A novel thermostable nitrilase superfamily amidase from Geobacillus pallidus showing acyl transfer activity

Makhongela

Głowacka

Agarkar

et al. 2007

Appl Microbiol Biotechnol

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An amidase (EC 3.5.1.4) in branch 2 of the nitrilase superfamily, from the thermophilic strain Geobacillus pallidus RAPc8, was produced at high expression levels (20 U/mg) in small-scale fermentations of Escherichia coli. The enzyme was purified to 90% homogeneity with specific activity of 1,800 U/mg in just two steps, namely, heat-treatment and gel permeation chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and electron microscopic (EM) analysis of the homogenous enzyme showed the native enzyme to be a homohexamer of 38 kDa subunits. Analysis of the biochemical properties of the amidase showed that the optimal temperature and pH for activity were 50 and 7.0°C, respectively. The amidase exhibited high thermal stability at 50 and 60°C, with half-lives greater than 5 h at both temperatures. At 70 and 80°C, the half-life values were 43 and 10 min, respectively. The amidase catalyzed the hydrolysis of low molecular weight aliphatic amides, with D-selectivity towards lactamide. Inhibition studies showed activation/inhibition data consistent with the presence of a catalytically active thiol group. Acyl transfer reactions were demonstrated with acetamide, propionamide, isobutyramide, and acrylamide as substrates and hydroxylamine as the acyl acceptor; the highest reaction rate being with isobutyramide. Immobilization by entrapment in polyacrylamide gels, covalent binding on Eupergit C beads at 4°C and on Amberlite-XAD57 resulted in low protein binding and low activity, but immobilization on Eupergit C beads at 25°C with cross-linking resulted in high protein binding yield and high immobilized specific activity (80% of non-immobilized activity). Characterization of Eupergit C-immobilized preparations showed that the optimum reaction temperature was unchanged, the pH range was somewhat broadened, and stability was enhanced giving half-lives of 52 min at 70°C and 30 min at 80°C. The amidase has potential for application under high temperature conditions as a biocatalyst for D-selective amide hydrolysis producing enantiomerically pure carboxylic acids and for production of novel amides by acyl transfer.

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Study of the amidase signature group

Cited by 129 publications

References 38 publications

On the Evolution of the tRNA-Dependent Amidotransferases, GatCAB and GatDE

On the Evolution of the tRNA-Dependent Amidotransferases, GatCAB and GatDE

Molecular Identification of a Functional Homologue of the Mammalian Fatty Acid Amide Hydrolase in Arabidopsis thaliana

A novel thermostable nitrilase superfamily amidase from Geobacillus pallidus showing acyl transfer activity

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