Evolution of structure and substrate specificity ind-alanine:d-Alanine ligases and related enzymes

Evers, Stefan; Casadewall, Barbara; Charles, Murielle; Dutka‐Malen, Sylvie; Galimand, Marc; Courvalin, Patrice

doi:10.1007/bf02338803

Cited by 74 publications

(62 citation statements)

References 32 publications

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“…Interestingly, two of these associated proteins were assigned with functions that can be associated with the biosynthesis of the cell wall: dTDT-glucose-4,6-dehydratase (4,6-dehydratase), which catalyzes the irreversible conversion of dDTD-glucose to dTDT-4-keto-6-deoxyglucose (29), and D-alanine:D-alanine ligase, which is an ATP-dependent enzyme that promotes dipeptide formation of D-Ala-DAla (1). The 6-deoxysugars are principle components of bacterial lipopolysaccharides (24), and in many prokaryotes D-Ala-D-Ala is incorporated into UDP-muramyl pentapeptide, which ultimately is used to produce peptidoglycan polymers (10).…”

Section: Discussionmentioning

confidence: 99%

Effect of Adaptation to Ethanol on Cytoplasmic and Membrane Protein Profiles of Oenococcus oeni

Silveira

Baumgärtner

Rombouts

et al. 2004

Appl Environ Microbiol

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The practical application of commercial malolactic starter cultures of Oenococcus oeni surviving direct inoculation in wine requires insight into mechanisms of ethanol toxicity and of acquired ethanol tolerance in this organism. Therefore, the site-specific location of proteins involved in ethanol adaptation, including cytoplasmic, membrane-associated, and integral membrane proteins, was investigated. Ethanol triggers alterations in protein patterns of O. oeni cells stressed with 12% ethanol for 1 h and those of cells grown in the presence of 8% ethanol. Levels of inosine-5-monophosphate dehydrogenase and phosphogluconate dehydrogenase, which generate reduced nicotinamide nucleotides, were decreased during growth in the presence of ethanol, while glutathione reductase, which consumes NADPH, was induced, suggesting that maintenance of the redox balance plays an important role in ethanol adaptation. Phosphoenolpyruvate:mannose phosphotransferase system (PTS) components of mannose PTS, including the phosphocarrier protein HPr and EII Man , were lacking in ethanol-adapted cells, providing strong evidence that mannose PTS is absent in ethanoladapted cells, and this represents a metabolic advantage to O. oeni cells during malolactic fermentation. In cells grown in the presence of ethanol, a large increase in the number of membrane-associated proteins was observed. Interestingly, two of these proteins, dTDT-glucose-4,6-dehydratase and D-alanine:D-alanine ligase, are known to be involved in cell wall biosynthesis. Using a proteomic approach, we provide evidence for an active ethanol adaptation response of O. oeni at the cytoplasmic and membrane protein levels.

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Section: Discussionmentioning

confidence: 99%

Effect of Adaptation to Ethanol on Cytoplasmic and Membrane Protein Profiles of Oenococcus oeni

Silveira

Baumgärtner

Rombouts

et al. 2004

Appl Environ Microbiol

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“…Although the consensus sequence of the -loop in these DDLs is Ser (or Ala or Thr)-Lys-Tyr-Ile (or Met or Ser) (31), the loop in the S. lavendulae DDL is Ala-Lys-Tyr-Gln. The Gln residue, present in the -loop, is characteristic of D-Ala-D-Ser ligases, which belong to VanC, found in vancomycin-resistant bacteria (31,32).…”

Section: Cloning Of Genes Encoding the Dcs Resistancementioning

confidence: 99%

Self-protection Mechanism in d-Cycloserine-producing Streptomyces lavendulae

Noda

Kawahara

Ichikawa

et al. 2004

Journal of Biological Chemistry

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An antibiotic, D-cycloserine (DCS), inhibits the catalytic activities of alanine racemase (ALR) and D-alanyl-D-alanine ligase (DDL), which are necessary for the biosynthesis of the bacterial cell wall. In this study, we cloned both genes encoding ALR and DDL, designated alrS and ddlS, respectively, from DCS-producing Streptomyces lavendulae ATCC25233. Each gene product was purified to homogeneity and characterized. Escherichia coli, transformed with a pET vector carrying alrS or ddlS, displays higher resistance to DCS than the same host carrying the E. coli ALR-or DDL-encoded gene inserted into the pET vector. Although the S. lavendulae DDL was competitively inhibited by DCS, the K i value (920 M) was obviously higher (40ϳ100-fold) than those for E. coli DdlA (9 M) or DdlB (27 M). The high K i value of the S. lavendulae DDL suggests that the enzyme may be a self-resistance determinant in the DCS-producing microorganism. Kinetic studies for the S. lavendulae ALR suggest that the time-dependent inactivation rate of the enzyme by DCS is absolutely slower than that of the E. coli ALR. We conclude that ALR from DCS-producing S. lavendulae is also one of the self-resistance determinants.

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“…While the ribosome system is universal, other machineries specific for certain peptides are also known, including nonribosomal peptide synthetase (NRPS) (4,5,26), folylpolyglutamate synthase (23), enzymes involved in bacterial peptidoglycan biosynthesis (17,27), poly-␥-glutamate synthetase (2,25), cyanophycin synthetase (1), D-alanine:D-alanine ligase (DDL) (6,27), and so on.…”

mentioning

confidence: 99%

ywfEinBacillus subtilisCodes for a Novel Enzyme,l-Amino Acid Ligase

Tabata

Ikeda²,

Hashimoto³

2005

J Bacteriol

113

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The ATP-dependent carboxylate-amine/thiol ligase superfamily is known to contain enzymes catalyzing the formation of various types of peptide, such as D-alanyl-D-alanine, polyglutamate, and ␥-peptide, but, curiously, no enzyme synthesizing ␣-dipeptides of L-amino acids is known. We attempted to find such an enzyme. By in silico screening based on the consensus sequence of the superfamily followed by an in vitro assay with purified enzyme to avoid the degradation of the peptide(s) synthesized, ywfE of Bacillus subtilis was found to code for the activity forming L-alanyl-L-glutamine from L-alanine and L-glutamine with hydrolysis of ATP to ADP. No AMP was formed, supporting the idea that the enzyme belongs to the superfamily. Surprisingly, the enzyme accepted a wide variety of L-amino acids. Among 231 combinations of L-amino acids tested, reaction products were obtained for 111 combinations and 44 kinds of ␣-dipeptides were confirmed by high-performance liquid chromatography analyses, while no tripeptide or longer peptide was detected and the D-amino acids were inert. From these results, we propose that ywfE encodes a new member of the superfamily, L-amino acid ligase.

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Evolution of structure and substrate specificity ind-alanine:d-Alanine ligases and related enzymes

Cited by 74 publications

References 32 publications

Effect of Adaptation to Ethanol on Cytoplasmic and Membrane Protein Profiles of Oenococcus oeni

Effect of Adaptation to Ethanol on Cytoplasmic and Membrane Protein Profiles of Oenococcus oeni

Self-protection Mechanism in d-Cycloserine-producing Streptomyces lavendulae

ywfEinBacillus subtilisCodes for a Novel Enzyme,l-Amino Acid Ligase

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