"Open" structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase.

UDP-N-acetylmuramoyl-l-alanine:d-glutamate (MurD) ligase catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine (UMA). The crystal structures of Escherichia coli in the substrate-free form and MurD complexed with UMA have been determined at 2.4 A and 1.88 A resolution, respectively. The MurD structure comprises three domains each of a topology reminiscent of nucleotide-binding folds. In the two structures the C-terminal domain undergoes a large rigid-body rotation away from the N-terminal and central domains. These two "open" structures were compared with the four published "closed" structures of MurD. In addition the comparison reveals which regions are affected by the binding of UMA, ATP and d-Glu. Also we compare and discuss two structurally characterized enzymes which belong to the same ligase superfamily: MurD and folylpolyglutamate synthetase (FGS). The analysis allows the identification of key residues involved in the reaction mechanism of FGS. The determination of the two "open" conformation structures represents a new step towards the complete elucidation of the enzymatic mechanism of the MurD ligase.

Determination of the MurD mechanism through crystallographic analysis of enzyme complexes.

UDP -N- acetylmuramoyl- L -alanine: D -glutamate (MurD) ligase catalyses the addition of d -glutamate to the nucleotide precursor UDP -N- acetylmuramoyl- L -alanine (UMA). The crystal structures of three complexes of Escherichia coli MurD with a variety of substrates and products have been determined to high resolution. These include (1) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mg2+, (2) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mn2+, and (3) the binary complex of MurD with the product UDP - N- acetylmuramoyl- L -alanine- D -glutamate (UMAG). The reaction mechanism supported by these structures proceeds by the phosphorylation of the C-terminal carboxylate group of UMA by the gamma-phosphate group of ATP to form an acyl-phosphate intermediate, followed by the nucleophilic attack by the amino group of D-glutamate to produce UMAG. A key feature in the reaction intermediate is the presence of two magnesium ions bridging negatively charged groups.

Formation of adenosine 5'-tetraphosphate from the acyl phosphate intermediate: a difference between the MurC and MurD synthetases of Escherichia coli.

The mechanism of the Mur synthetases of peptidoglycan biosynthesis is thought to involve in each case the successive formation of an acyl phosphate and a tetrahedral intermediate. The existence of the acyl phosphates for the MurC and MurD enzymes from Escherichia coli was firmly established by their in situ reduction by sodium borohydride followed by acid hydrolysis, yielding the corresponding amino alcohols. Furthermore, it was found that MurD, but not MurC, catalyses the synthesis of adenosine 5'-tetraphosphate from the acyl phosphate, thereby substantiating its existence and pointing out a difference between the two enzymes.

Effect of analogues of diaminopimelic acid on the meso-diaminopimelate-adding enzyme from Escherichia coli.

Several analogues of diaminopimelic acid (A2pm) were tested as substrates or inhibitors of the meso-diaminopimelate-adding enzyme from Escherichia coli. They included lanthionine derivatives, a phosphonic analogue, heterocyclic compounds, 3-fluoro-A2pm, 4-methylene-A2pm and N-hydroxy-A2pm. The best substrates were, in decreasing order of specific enzyme activity, (2S,3R,6S)-3-fluoro-A2pm, meso-lanthionine sulfoxide and N-hydroxy-A2pm (mixture of stereoisomers). In those cases where all the stereoisomers were available, the specificity could be described as meso > > DD approximately to LL. N-Hydroxy-A2pm (mixture of stereoisomers) strongly inhibited the addition of radioactive meso-A2pm to UDP-N-acetylmuramoyl-dipeptide.

Site-directed mutagenesis and chemical modification of the two cysteine residues of the UDP-N-acetylmuramoyl:L-alanine ligase of Escherichia coli.

Site-directed mutagenesis and chemical modification of the two cysteine residues of the MurC L-alanine-adding enzyme from Escherichia coli were undertaken to study their possible role in activity and stability. Their replacement by alanine was not critical for activity. However, C230 played a role in enzyme stability and substrate binding. N-Ethylmaleimide alkylation led to monoalkylated and dialkylated proteins. The monoalkylated protein had mostly unmodified C230 residues. The extent of alkylation of C230 paralleled the loss of activity, whereas that of C426 did not. Protection against inactivation by beta,gamma-imidoadenosine 5'-triphosphate implied the involvement of C230 in the ATP binding site.

Synthesis of the monomer and dimer peptide fragments of the Micrococcus lysodeikticus cell wall peptidoglycan.

Three branched peptides, namely pentapeptide A and the two decapeptides B and C corresponding respectively to the monomer and the two dimer peptide fragments of the M. lysodeikticus cell wall peptidoglycan, were synthetized by adequate methods of peptide synthesis in homogeneous phase. The synthetized peptides showed the same electrophoretic and chromatographic behavior as the natural peptide fragments. Only decapeptide B was hydrolysed by the Myxobacter AL-1 protease by cleavage of the D-Ala-L-Ala bond and inversely, only decapeptide C was digested by the Streptomyces albus ML endopeptidase by cleavage of the D-Ala-epsilon-Lys linkage. In both enzymatic hydrolyses the pentapeptide monomer was formed.

[Radioactive analogs of neurotensin. II. Preparation of tritiated neurotensin from a synthetic multi-unsaturated derivative]. / Analogues radioactifs de la neurotensine. II. Préparation de neurotensine tritiée à partir d'un dérivé multi-insaturé de synthèse.

In this second paper on the synthesis of neurotensin analogues as precursors for radiolabelling, solid phase synthesis of two polyunsaturated peptides, [Dah6, delta Pro7,10]-neurotensin and acetyl-[delta Pro10]-neurotensin-(8-13), are described. The first one contains one triple bond and two double bonds susceptible to tritiation in the same molecule, the second one contains one double bond in the shortest sequence having neurotensin activity. The C-terminal residue, Boc-Leu, was esterified on the chloromethyl-resin by its cesium salt. For the other amino acids a double coupling was carried out, the first one with dicyclohexylcarbodimide and the second one with the amino acid hydroxybenzotriazole ester. Acylation of the second amino acid, on the resin, presented some difficulties to achieve completeness and several acetylations and benzoylations had to be performed in order to block the last 4 per cent of free amines. It seems that these difficulties are related to some batches of chloromethyl-resin. Incorporation of both acetylenic lysine, N alpha-Boc-N epsilon-Z-L-2,6-diamino-4-hexynoic acid, whose synthesis is described, and N alpha-Boc-L-3,4-dehydroproline was without problems in this synthesis. After cleavage by hydrofluoric acid the crude peptides were purified by gel filtration on Bio-Gel P2 and ion exchange chromatography on carboxymethylcellulose (CM 52). [Dah6, delta Pro7,10]-neurotensin so obtained (51 per cent compared to starting Boc-Leu-resin) was in homogeneous form as characterized by amino acid analysis, thin layer chromatography in different systems and high performance liquid chromatography. The hydrogenation or tritiation product was identical with native neurotensin. Unsaturated derivative and neurotensin obtained after catalytic hydrogenation were as active as native neurotensin in inhibition of 125I-[Trp11]-neurotensin binding to rat brain synaptic membranes and in guinea pig ileum contractility test. Substitution of proline and lysine by their dehydro-derivatives did not affect the biological properties of neurotensin. The tritiated neurotensin (160-180 Ci/mmol) should be a good agent for biological characterization of neurotensin receptors and for investigation of the peptide metabolism.

Study of the overproduced uridine-diphosphate-N-acetylmuramate:L-alanine ligase from Escherichia coli.

The UDP-N-acetylmuramate:L-alanine ligase of Escherichia coli is responsible for the addition of the first amino acid of the peptide moiety in the assembly of the monomer unit of peptidoglycan. It catalyzes the formation of the amide bond between UDP-N-acetylmuramic acid (UDP-MurNAc) and L-alanine. The UDP-MurNAc-L-alanine ligase was overproduced 2000-fold in a strain harboring a recombinant plasmid (pAM1005) with the murC gene under the control of the inducible promoter trc. The murC gene product appears as a 50-kDa protein accounting for ca. 50% of total cell proteins. A two-step purification led to 1 g of a homogeneous protein from an 8-liter culture. The N-terminal sequence of the purified protein correlated with the nucleotide sequence of the gene. The stability of the enzymatic activity is strictly dependent on the presence of 2-mercaptoethanol. The K(m) values for substrates UDP-N-acetylmuramic acid, L-alanine, and ATP were estimated; 100, 20, and 450 microM, respectively. The specificity of the enzyme for its substrates was investigated with various analogues. Preliminary experiments attempting to elucidate the enzymatic mechanism were consistent with the formation of an acylphosphate intermediate.

Study of the reaction mechanism of the D-glutamic acid-adding enzyme from Escherichia coli.

The D-glutamic acid-adding enzyme of Escherichia coli, or MurD, was purified from an overproducing strain and a few aspects of its reaction mechanism were studied. The existence of a reactive cysteinyl residue was shown by the following experiments: (1) two thiol-modifying reagents, (5,5'-dithiobis)2-nitrobenzoic acid and 2-nitro-5-thiocyanobenzoic acid, inactivated the enzyme; (2) incubation with tetranitromethane led to inactivation and to the appearance of cysteic acid (not to 3-nitrotyrosine); (3) in each case, ATP or UDP-MurNAc-L-Ala (but not D-glutamic acid) protected the enzyme from inactivation. The existence of a reactive lysyl residue was shown by the action of 2,4,6-trinitrobenzenesulfonic acid, a reagent specific for lysyl residues present in phosphate-binding sites. The formation of an acyl phosphate intermediate was consistent with three types of results: (1) the molecular isotope exchange reaction, which took place only in the presence of phosphate, but which was not strictly dependent on the presence of ADP; (2) a release of phosphate, measured by the molybdate assay, observed when the enzyme was incubated with ATP and UDP-MurNAc-L-Ala (without D-glutamic acid); (3) the appearance of a new radioactive compound (besides ATP and Pi) after incubation for a few minutes with UDP-MurNAc-L-Ala and [gamma-32P]ATP. Finally, the fact that phosphinate 1 was a good inhibitor of the enzyme (IC50 = 0.7 microM) strongly suggested that a tetrahedral transition state follows the acyl phosphate in the reaction pathway.

Effect of various alanine analogues on the L-alanine-adding enzyme from Escherichia coli.

An extract from Escherichia coli containing the L-alanine-adding enzyme with a high specific activity was prepared. Several compounds structurally related to L-alanine were tested as inhibitors of this activity. Intact amino and carboxyl groups were necessary for an interaction with the enzyme. Certain halogenated (haloalanines) or unsaturated (L-vinylglycine, L-propargylglycine, 3-cyano-L-alanine) amino acids were good inhibitors. Radioactive glycine, serine and 1-aminoethylphosphonic acid were tested as substrates. Whereas glycine or L-serine gave rise to the formation of the corresponding nucleotide product, no synthesis of UDP-N-acetylmuramyl-L-1-aminoethylphosphonic acid could be detected.

Effect of various analogues of D-glutamic acid on the D-glutamate-adding enzyme from Escherichia coli.

Twenty-four analogues of D-glutamic acid were tested as substrates or inhibitors of the D-glutamate-adding enzyme from Escherichia coli. The best substrates were, in decreasing order of specific activity, D-erythro-4-methylglutamic acid, D-erythro-3-methylglutamic acid, DL-homocysteic acid, (+/-)-trans-1-amino-3-carboxy-cyclopentanecarboxylic acid and (+/-)-trans-1-amino-3-carboxy-cyclohexanecarboxylic acid. Among the different stereoisomers, only the D-erythro isomers for methylglutamic acids, and the trans isomers for the cyclic analogs, were substrates. Apart from the D-erythro-3- and 4-methylglutamic acids and DL-homocysteic acid, none of the examined compounds significantly inhibited the addition of radioactive D-glutamic acid to UDP-N-acetylmuramyl-L-alanine.

Synthesis and biochemical evaluation of some novel N-acyl phosphono- and phosphinoalanine derivatives as potential inhibitors of the D-glutamic acid-adding enzyme.

A series of N-(5-phthalimidopentanoyl)-, N-[2-(2-ethoxy)acetyl]-, and N-(7-oxooctanoyl)-phosphono and phosphinoalanine derivatives has been synthesized and evaluated for inhibition of the D-glutamic acid-adding enzyme (MurD) of peptidoglycan biosynthesis.

Properties of synthetic ferrihydrite as an amino acid adsorbent and a promoter of peptide bond formation.

Ferrihydrite, an iron oxide hydroxide, is found in all kinds of environments, from hydrothermal hot springs to extraterrestrial materials. It has been shown that this material is nanoporous, and because of its high surface area, it has outstanding adsorption properties and in some cases catalysis properties. In this work we studied the adsorption properties of ferrihydrite with respect to amino acids. Samples of pure ferrihydrite were synthesised and exposed to solutions of amino acids including both proteinaceous and non-proteinaceous species. These experiments revealed important characteristics of this mineral as both an adsorbent of amino acids and a promoter of peptide bond formation.

Synthesis of tritiated tuftsin and macrophage inhibitory tripeptide via acetylenic intermediates.

Acetylenic analogues of tuftsin (Thr-Dah-Pro-Arg) and of a macrophage inhibitory tripeptide (Thr-Dah-Pro) have been synthesized by conventional procedures in solution (Dah = 2,6-diamino-4-hexynoic acid). These acetylenic derivatives are intermediates for the preparation of structurally unmodified, tritiated peptides. Catalytic tritiation of Thr-Dah-Pro-Arg and of Thr-Dah-Pro has afforded the radioactive tetra- and tripeptides with specific activities of 11.4 Ci/mmol and 37 Ci/mmol, respectively.

Replacement of diaminopimelic acid by cystathionine or lanthionine in the peptidoglycan of Escherichia coli.

In Escherichia coli, auxotrophy for diaminopimelic acid (A2pm) can be suppressed by growth with exogenous cystathionine or lanthionine. The incorporation of cystathionine into peptidoglycan metabolism was examined with a dapA metC mutant, whereas for lanthionine, a dapA metA mutant strain was used. Analysis of peptidoglycan precursors and sacculi isolated from cells grown with epimeric cystathionine or lanthionine showed that meso-A2pm was totally replaced in the same position by either sulfur-containing amino acid. Moreover, mainly L-allo-cystathionine (95%) or meso-lanthionine (93%) was incorporated into the precursors and sacculi. For this purpose, a new, efficient high-pressure liquid chromatography (HPLC) technique for analysis of the cystathionine isomers was developed. The formation of the UDP-MurNAc tripeptide appeared to be a critical step, since the MurE synthetase accepted meso-lanthionine or D-allo- or L-allo-cystathionine in vitro as good substrates, although with higher Km values. Presumably, the 10-fold-higher UDP-MurNAc-L-Ala-D-Glu pool of cells grown with cystathionine or lanthionine ensured a normal rate of synthesis. The kinetic parameters of the MurF synthetase catalyzing the addition of D-alanyl-D-alanine were very similar for the meso-A2pm-,L-allo-cystathionine-, and meso-lanthionine-containing UDP-MurNAc tripeptides. HPLC analysis of the soluble fragments resulting from 95% digestion by Chalaropsis N-acetylmuramidase of the peptidoglycan material in isolated sacculi revealed that the proportion of the main dimer was far lower in cystathionine and lanthionine sacculi.

Partial purification and specificity studies of the D-glutamate-adding and D-alanyl-D-alanine-adding enzymes from Escherichia coli K12.

The D-glutamate-adding and D-alanyl-D-alanine-adding enzymes from Escherichia coli were partially purified by fast protein liquid chromatography on an anion exchanger. Their relative molecular masses, determined by gel filtration on Superose 12, were 54,000 +/- 2000 and 51,000 +/- 2000, respectively. In order to investigate the specificity of these ligases, several compounds derived from their respective nucleotide substrates were prepared. In the case of the D-Glu-adding enzyme, DDP-MurNAc-L-Ala (DDP = dihydrouridine 5'-diphosphate) and P1-MurNAc-L-Ala were substrates of the reaction. In the case of the D-Ala-D-Ala-adding enzyme, only DDP-MurNAc-L-Ala-D-Glu(-meso-A2pm) was a substrate; P1-MurNAc-L-Ala-D-Glu(-meso-A2pm) was neither a substrate nor an inhibitor. Concerning the amino acid site of the D-Glu-adding enzyme, even closely related analogues of D-glutamate hardly inhibited the reaction.

Synthesis and use of peptide substrates for the isolation and characterization of proenkephalin processing enzymes.

Classical methods of peptide synthesis in solution were used for the preparation of the two tetrapeptides alanyl-lysyl-arginyl-tyrosine and acetyl-alanyl-lysyl-arginyl-tyrosine-(N-methylamide). The two compounds were able to be recognized as substrates by proenkephalin processing enzymes and were used for the development of a quantitative assay for these enzymes. The first substrate proved to be convenient, although it was also partially degraded by amino- and carboxypeptidases under the conditions of the assay. The second was found to be hydrolyzed by the endopeptidases at too slow a rate to allow its routine use in the assay.

Synthesis of analogs of the serum thymic nonapeptide, "facteur thymique serique" (FTS). Part I.

Analogs of FTS (Facteur Thymique Sérique), less than :formula: (see text), a circulating thymic factor, were prepared by replacing the amino acid residues in positions 1, 2, 8 and 9, or by shortening the nonapeptide chain at the N- or C-terminal end. These peptides were synthesized by two different schemes using the conventional synthesis in solution.

The nitrogen source-dependent 126-kDa protein from Synechococcus PCC 7942 plasmalemma: a trimer of the NrtA nitrate-binding protein.

Expression of a 126-kDa protein in the plasmalemma (cytoplasmic membrane) from Synechococcus PCC 7942 is dependent on the nitrogen source. Polyclonal antibody raised against the NrtA protein reacted with the 126-kDa protein. Two peptide sequences from the 126-kDa protein were retrieved in NrtA. FPLC purification of plasmalemma solubilised in Triton X-100 gave a fraction consisting mainly of a 126-kDa component (72.6%), as shown by sedimentation velocity. Equilibrium sedimentation of the same fraction gave evidence of the existence of an oligomeric structure (Ka = 2 x 10(3) and 2.9 subunits). Thus, the 126-kDa protein is considered as a trimeric arrangement of the 45-kDa protein in the plasmalemma.

Peptides containing 2-aminopimelic acid. Synthesis and study of in vitro effects on bacterial cells.

Taking advantage of the peptide transport strategy, we have designed and synthesized several new peptides containing 2-aminopimelic acid (Apm), an inhibitor of the diaminopimelate pathway in bacteria: L-Lys-ambo-Apm, ambo-Apm-L-Lys, L-Lys-L-Ala-ambo-Apm, ambo-Apm-L-Ala-L-Lys, L-Ala(Cl)-ambo-Apm and ambo-Apm-L-Ala(Cl). In the two latter cases, Apm was associated with antibacterial amino acid beta-chloro-L-alanine [L-Ala(Cl)], an inhibitor of alanine racemase and transaminase B. The peptides displayed weak or no antibacterial activities; nevertheless, those containing L-Ala(Cl) had low MIC values in the presence of amino acids restoring protein synthesis. When tested on exponential phase Escherichia coli cells grown in minimal medium, the peptides were without effect or bacteriostatic, but important bacteriolytic effects could be observed, especially for the L-Ala(Cl)-containing peptides, when the growth medium was supplemented with specific amino acids. It was demonstrated that the weak or nil effect of the L-lysine-containing peptides was due to a poor uptake.