D-alanine Carboxypeptidase Activity Research Articles

Substitution of lysine 213 with arginine in penicillin-binding protein 5 of Escherichia coli abolishes D-alanine carboxypeptidase activity without affecting penicillin binding.

All penicillin-binding proteins (PBPs) contain a conserved box of homology in the carboxyl-terminal half of their primary sequence that can be Lys-Thr-Gly, Lys-Ser-Gly, or His-Thr-Gly. Site-saturation mutagenesis was used to address the role of the lysine residue at this position (Lys213) in Escherichia coli PBP 5, a D-alanine carboxypeptidase enzyme. A soluble form of PBP 5 was used to replace Lys213 with 18 other amino acids, and the ability of these mutant proteins to bind [3H]penicillin G was assessed. Only the substitution of lysine with arginine resulted in a protein that was capable of forming a stable covalent complex with antibiotic. The affinity of [14C]penicillin G for the arginine mutant was 1.2-fold higher than for wild-type PBP 5 (4.4 versus 5.1 micrograms/ml for 20 min at 30 degrees C), and both proteins showed identical rates of hydrolysis of the [14C]penicilloyl-bound complex (t1/2 = 9.1 min). Surprisingly, the arginine-substituted protein was unable to catalyze D-alanine carboxypeptidase activity in vitro, which suggests that there is a substantial difference in the geometries of the peptide substrate and penicillin G within the active site of PBP 5.

Substitution of lysine 213 with arginine in penicillin-binding protein 5 of Escherichia coli abolishes D-alanine carboxypeptidase activity without affecting penicillin binding

Substitution of lysine 213 with arginine in penicillin-binding protein 5 of Escherichia coli abolishes D-alanine carboxypeptidase activity without affecting penicillin binding

Site-directed mutants of a soluble form of penicillin-binding protein 5 from Escherichia coli and their catalytic properties.

Soluble, truncated mutant and wild-type forms of penicillin-binding protein 5 (sPBP 5) from Escherichia coli were produced in large amounts by placing the dacA gene that encodes PBP 5 under the control of the trp-lac fusion promoter. The 3' end of the dacA gene used in this study contains a stop codon that results in the deletion of 15 amino acids from the carboxyl terminus and the production of a soluble protein. Using oligonucleotide-directed mutagenesis, the role of cysteine 115 in the mechanism of sPBP 5 was investigated. Alkylation of cysteine 115 with sulfhydryl reagents has previously been shown to inhibit severely the D-alanine carboxypeptidase activity of PBP 5. Alkylation also inhibits the hydrolysis of bound penicillin G, with only a slight effect on its binding. Cysteine 115 in sPBP 5 was changed to either a serine (sPBP 5C-S) or an alanine (sPBP 5C-A) residue. The wild-type and mutant sPBPs were purified in milligram amounts from induced cultures by ampicillin affinity chromatography. The mutant PBPs showed only a 2-fold increase in the half-life of the penicilloyl-PBP complex, and had a binding affinity for penicillin G identical to wild-type PBP 5. The Km for the release of D-alanine from the peptide L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala was 5.0, 3.5, and 7.8 mM for PBP 5, PBP 5C-S, and PBP 5C-A, respectively, while the values for Vmax were 2.5, 3.3, and 5.1 mumol/min/mg. From these data it was concluded that the cysteine residue does not directly participate in the enzymatic mechanism.

Reduced heat resistance of mutant spores after cloning and mutagenesis of the Bacillus subtilis gene encoding penicillin-binding protein 5.

Part of the gene encoding penicillin-binding protein 5 from Bacillus subtilis 168 was cloned in Escherichia coli with a synthetic oligonucleotide as a hybridization probe. The gene was designated dacA by analogy with E. coli. The nucleotide sequence was determined, and the predicted molecular mass was 45,594 daltons (412 amino acids). A comparison of the predicted amino acid sequence with that of the E. coli penicillin-binding protein 5 indicated that these enzymes showed about 25% identity. The B. subtilis dacA gene was mutated by integration of a plasmid into the structural gene by homologous recombination. A comparison of the mutant and control strains revealed that (i) the mutant lacked detectable penicillin-binding protein 5, (ii) the D-alanine carboxypeptidase activity of membranes isolated from the mutant was only 5% of that measured in membranes from the control strain, (iii) the mutant cells showed apparently normal morphology only during exponential growth, and after the end of exponential phase the cells became progressively shorter, (iv) the mutant sporulated normally except that the forespore occupied about two-thirds of the mother cell cytoplasm and, during its development, migrated towards the center of the mother cell, and (v) purified mutant spores were 10-fold less heat resistant but possessed normal refractility and morphology. Preliminary chemical analysis indicated that the structure of the cortex of the mutant was different.

Mutation in Pseudomonas aeruginosa causing simultaneous defects in penicillin-binding protein 5 and in enzyme activities of penicillin release and D-alanine carboxypeptidase.

Penicillin-binding protein 5 in Pseudomonas aeruginosa had moderately penicillin-sensitive D-alanine carboxypeptidase activity. As in Escherichia coli, a defect in this enzyme activity was not lethal.

Purification and properties of penicillin-binding proteins 5 and 6 from the dacA mutant strain of Escherichia coli (JE 11191).

Penicillin-binding proteins 5 and 6 have been purified to homogeneity from the dacA mutant strain of Escherichia coli (JE 11191). Protein 6 from the mutant strain appears to be identical to that from the wild type, but protein 5 is a mutant protein which has no D-alanine carboxypeptidase activity. Moreover, the mutant protein 5 binds, but does not release, [14C]penicillin G. Correspondingly, an acyl-enzyme intermediate derived from a synthetic substrate is accumulated by the mutant protein. A comparison of the acylation site for the synthetic substrate and for penicillin G by limited proteolysis and some other properties of the mutant protein are described.

Murein structure and lack of DD- and LD-carboxypeptidase activities in Caulobacter crescentus.

High-pressure liquid chromatography of a muramidase digest of murein sacculi from Caulobacter crescentus showed that the absence of D-alanine carboxypeptidase activity in the cells was reflected by a very high content of pentapeptide in the murein. Approximately half of the pentapeptide side chains were shown to contain glycine, which replaced D-alanine as the terminal amino acid.

Linear, uncross-linked peptidoglycan secreted by penicillin-treated Bacillus subtilis. Isolation and characterization as a substrate for penicillin-sensitive D-alanine carboxypeptidases.

Incubation of growing Bacillus subtilis with penicillin G led to the secretion of a peptidoglycan-related polymer and a nonglycan-bound pentapeptide into the culture medium. The secreted polymer was isolated and characterized as a linear cell wall glycan strand substituted predominantly by uncross-linked pentapeptide side chains. Polymer formation and secretion are most likely the result of continued synthesis and elongation of nascent glycan strands in the absence of subsequent processing by peptidoglycan transpeptidase or D-alanine carboxypeptidase enzymes. The nonglycan-bound pentapeptide, L-Ala-D-iso-Glu-meso-diaminopimelic acid-D-Ala-D-Ala, was probably formed by an N-acetylmuramyl-L-alanine amidase active on the peptide side chains of The uncross-linked polymer. The uncross-linked peptidoglycan polymer was shown to be a good substrate for penicillin-sensitive D-alanine carboxypeptidases purified from membranes of B. subtilis, Bacillus stearothermophilus, and Escherichia coli. D-alanine release was not, however, coupled to the cross-linking of peptide side chains, suggesting that these enzymes do not function as peptidoglycan transpeptidases in vivo. No transpeptidase or D-alanine carboxypeptidase activity was detected in mixtures of high molecular weight penicillin-binding proteins from B. subtilis, B. stearothermophilus, or Staphylococcus aureus. Possible reasons for the inability to demonstrate these activities are discussed. In addition, an N-acetylmuramyl-L-alanine amidase activity which copurifies with penicillin-binding proteins from B. subtilis, S. aureus, and E. coli was partially characterized.

On the process of cellular division in Escherichia coli: isolation and characterization of penicillin-binding proteins 1a, 1b, and 3.

Multiple mutants of Escherichia coli defective in penicillin-binding proteins (PBPs) were constructed, and into these strains Co1E1 plasmids carrying the genes for PBP-1a, -1b, or -3 were introduced. From these plasmid-carrying strains, PBP-1a and -1b were purified by ampicillin-Sepharose affinity chromatography and PBP-3 by cephalexin-Sepharose affinity chromatography. Improved purification was achieved by differential elution with NH2OH. Purified PBP-1b synthesized murein when added to the membrane fraction of a PBP-1b-defective mutant, which by itself failed to support murein synthesis in vitro. The PBP-1b preparation was able to synthesize murein from the lipid intermediate extracted with chloroform/methanol but was unable to utilize UDP-linked precursors for murein synthesis. Murein synthesis was inhibited by vancomysin, ristocetin, moenomycin, and enduracidin, but not by beta-lactam antibiotics. The synthesized murein was shown to contain crosslinked muropeptides. Their crosslinking was abolished by action of beta-lactam antibiotics. The PBP-1a and -3 preparations showed substantially no activity for murein synthesis in the same reaction system. None of the three PBPs showed D-alanine carboxypeptidase activity with UDP-N-acetylmuramoyl-pentapeptide as substrate or endopeptidase activity with bis(disaccharide-peptide) as substrate.

Effect of piperacillin on D-alanine carboxypeptidase activities from Pseudomonas aeruginosa.

Membrane-bound D-alanine carboxypeptidase activity from Pseudomonas aeruginosa is very sensitive to inhibition by piperacillin.

Murein biosynthesis during a synchromous cell cycle of Escherichia coli B

The last stages of murein biosynthesis were studied in relation to the division cycle of Escherichia coli in cells synchronized by amino acid starvation (Ron et al., J. Bacteriol. 123:374--376, 1975). Murein synthesis and the activities of the D-alanine carboxypeptidase and transpeptidase were found to vary significantly during the cell cycle. Maximal synthesis and transpeptidation were observed immediately after cell division, whereas maximal D-alanine carboxypeptidase activity was detected before cell division. These results are in agreement with our earlier findings that before cell division there is a stage of increased hydrolysis of the C-terminal D-alanine moiety of newly synthesized murein strands.

Mutants of Escherichia coli lacking in highly penicillin-sensitive D-alanine carboxypeptidase activity.

Mutants of Escherichia coli lacking in the highly penicillin-sensitive enzyme activities of D-carboxy-peptidase, transpeptidase, and endopeptidase, and with the concomitant absence of penicillin-binding protein 4 of B.G. Spratt and A.B. Pardee [(1975) Nature 254, 516-517] were isolated. The defect of these mutants is ascribed to the lack of an enzyme, D-alanine carboxypeptidase Ib. Genetic mapping studies show the mutation (dacB) to be located at 68 min on the E. coli chromosome map. The dacB mutation results in the simultaneous loss of D-alanine carboxypeptidase and penicillin-binding protein 4. The mutants grew normally under a wide range of growth conditions. We conclude that the enzyme is not a necessary component for normal peptidoglycan biosynthesis in E. coli.

Purification to homogeneity and properties of two D-alanine carboxypeptidases I From Escherichia coli.

Three homogeneous preparations of D-alanine carboxypeptidases I have been obtained from Escherichia coli strain H2143, termed enzymes IA, IB, and IC. Enzyme IA purified from the membrane after extraction with Triton X-100 appeared on sodium dodecyl sulfate gel electrophoresis to be a polypeptide doublet whose monomer molecular weights were about 32,000 and 34,000. In addition to D-alanine carboxypeptidase activity, it catalyzed a transpeptidase reaction with several substrates, bound [14C]penicillin G, had a weak penicillinase activity, but was devoid of endopeptidase activity. Enzyme IB obtained from the membrane after LiCl extraction and enzyme IC obtained from the supernatant solution were either identical or extremely similar. They were composed of a single polypeptide whose monomer molecular weight was about 41,000. In addition to carboxypeptidase activity, they catalyzed an endopeptidase reaction, had weak penicillinase activity, and had very poor transpeptidase activity, but did not bind [14C]penicillin G. Some data relating to the mechanism of catalysis by these enzymes are described. Their possible physiological role is discussed.

The formation of functional penicillin-binding proteins

A method was developed which permitted determination of the [14C]benzylpenicillin and [14C]Cephapirin binding capacity of rapidly growing Bacillus subtilis cells in liquid culture. Over the concentration range of the binding plateau (0.1 to 0.8 mug/ml), [14C]benzylpenicillin significantly inhibited formation of functional penicillin-binding proteins, but had comparatively little effect on total bacterial protein synthesis. The data suggest that penicillin covalently bound to the cells in a chemically stable manner alone is not sufficient to inhibit formation of functional binding proteins and that unbound penicillin in the growth medium is necessary. The concentration of unbound antibiotic in the culture medium, in turn, is a function of the cell-bound penicillinase activity whose significance increases with cell density. [14C]Cephapirin, a cephalosporin resistant to this cell-bound penicillinase almost completely inhibited the formation of functional Cephapirin-binding proteins, but had relatively little effect on total protein synthesis. At concentrations 250-fold higher than that required to inhibit formation of functional binding proteins. Cephapirin did not inhibit particulate D-alanine carboxypeptidase activity and presumably did not bind covalently to this penicillin-binding protein.

Penicillin-sensitive Transpeptidation during Peptidoglycan Biosynthesis in Cell-free Preparations from Bacillus megaterium: II. EFFECT OF PENICILLINS AND CEPHALOSPORINS ON BACTERIAL GROWTH AND IN VITRO TRANSPEPTIDATION

Abstract The effect of penicillins and cephalosporins on the various transpeptidation reactions presented in the preceding paper is discussed. Inhibition by cloxacillin and penicillin G of [14C]diaminopimelic acid incorporation during peptidoglycan synthesis appeared to be partially reversible after the antibiotic was destroyed by treatment with penicillinase. Inhibition of the cross-linking reaction by cloxacillin appeared to be fully reversible. These and other results suggested the presence of more than one transpeptidase. In addition, a d-alanine carboxypeptidase activity present in the particulate enzyme preparation was examined and found to be irreversibly inhibited by penicillin G and relatively insensitive to cloxacillin. It is suggested that the transpeptidases(s) and the d-alanine carboxypeptidase are separate enzymes.

Biosynthesis of the Peptidoglycan of Bacterial Cell Walls: XVI. THE REVERSIBLE FIXATION OF RADIOACTIVE PENICILLIN G TO THE d-ALANINE CARBOXYPEPTIDASE OF BACILLUS SUBTILIS

Abstract A particulate d-alanine carboxypeptidase present in Bacillus subtilis has been studied. This enzyme has a pH optimum near 5, and is activated by Zn+2 cations. The enzyme is inactivated by penicillin G and activity cannot be restored by washing or by treating it with penicillinase. 14C-Penicillin G is also bound to this particulate enzyme. Both the binding of penicillin G and the inactivation of the carboxypeptidase by penicillin G are reversed by treatment with neutral hydroxylamine, and the kinetics of these two processes is identical. d-Alanine carboxypeptidase activity is also inhibited by sulfhydryl reagents such as iodoacetate in a manner similar to their inhibition of penicillin binding. The possibility that the particulate d-alanine carboxypeptidase may be an uncoupled transpeptidase is discussed.