Site-directed mutagenesis of proposed active-site residues of penicillin-binding protein 5 from Escherichia coli

Alignment of the amino acid sequence of penicillin-binding protein 5 (PBP5) with the sequences of other members of the family of active-site-serine penicillin-interacting enzymes predicted the residues playing a role in the catalytic mechanism of PBP5. Apart from the active-site (Ser44), Lys47, Ser110-Gly-Asn, Asp175 and Lys213-Thr-Gly were identified as the residues making up the conserved boxes of this protein family. To determine the role of these residues, they were replaced using site-directed mutagenesis. The mutant proteins were assayed for their penicillin-binding capacity and DD-carboxypeptidase activity. The Ser44Cys and the Ser44Gly mutants showed a complete loss of both penicillin-binding capacity and DD-carboxypeptidase activity. The Lys47Arg mutant also lost its DD-carboxypeptidase activity but was able to bind and hydrolyse penicillin, albeit at a considerably reduced rate. Mutants in the Ser110-Gly-Asn fingerprint were affected in both acylation and deacylation upon reaction with penicillin and lost their DD-carboxypeptidase activity with the exception of Asn112Ser and Asn112Thr. The Asp175Asn mutant showed wild-type penicillin-binding but a complete loss of DD-carboxypeptidase activity. Mutants of Lys213 lost both penicillin-binding and DD-carboxypeptidase activity except for Lys213His, which still bound penicillin with a k+2/K' of 0.2% of the wild-type value. Mutation of His216 and Thr217 also had a strong effect on DD-carboxypeptidase activity. Thr217Ser and Thr217Ala showed augmented hydrolysis rates for the penicillin acyl-enzyme. This study reveals the residues in the conserved fingerprints to be very important for both DD-carboxypeptidase activity and penicillin-binding, and confirms them to play crucial roles in catalysis.

Molecular structures of penicillin-binding proteins and beta-lactamases

In the past, new antibacterial agents have been selected either from natural sources or by 'trial and error' modification of existing antibacterials. Future therapeutic strategies are likely to depend on increased knowledge of existing drug targets and the search for new targets. The machinery for the assembly of bacterial-cell-wall peptidoglycan is an ideal place to look.

Relative specificities of a series of beta-lactam-recognizing enzymes towards the side-chains of penicillins and of acyclic thioldepsipeptides

In an attempt to understand more of the subtle differences between bacterial beta-lactamases and DD-peptidases, comparisons have been made between the specificities of these enzymes towards the phenylacetyl side chain, generally thought to be favoured by beta-lactamases, and the NN'-diacetyl-L-lysyl side chain, widely employed in low-molecular-mass substrates of DD-peptidases. These comparisons were carried out with both a penicillin and an acyclic thioldepsipeptide reaction nucleus and employing a range of both beta-lactamases and DD-peptidases. Rather contrary to general expectations, a general preference for reaction of both groups of enzymes with penicillins rather than thioldepsipeptides was observed and for the phenylacetyl rather than the NN'-diacetyl-L-lysyl side chain. Quantitative comparisons suggested that the side chains of penicillins may be bound in relatively similar sites in all of the enzymes whereas the side chains of thioldepsipeptides are more heterogeneously bound, both with respect to each other and to the comparable side chains of penicillins.

Crystallization and X-ray diffraction study of the Streptomyces K15 penicillin-binding DD-transpeptidase

The 262 amino acid residue long DD-transpeptidase/penicillin-binding protein of Streptomyces K15 has been crystallized at room temperature by using the hanging drop vapour diffusion technique. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit cell parameters a = 46.4 A, b = 54.1 A and c = 108.3 A. They contain one protein molecule per asymmetric unit and diffract to about 1.9 A. X-ray data have been collected to 2.0 A from a native crystal. The previously published amino acid sequence of the protein has been corrected at positions 71, 72, 113, 114 and 156.

The mechanism of action of DD-peptidases: the role of Threonine-299 and -301 in the Streptomyces R61 DD-peptidase

The side chains of residues Thr299 and Thr301 in the Streptomyces R61 DD-peptidase have been modified by site-directed mutagenesis. These amino acids are part of a beta-strand which forms a wall of the active-site cavity. Thr299 corresponds to the second residue of the Lys-Thr(Ser)-Gly triad, highly conserved in active-site beta-lactamases and penicillin-binding proteins (PBPs). Modification of Thr301 resulted only in minor alterations of the catalytic and penicillin-binding properties of the enzyme. No selective decrease of the rate of acylation was observed for any particular class of compounds. By contrast, the loss of the hydroxy group of the residue in position 299 yielded a seriously impaired enzyme. The rates of inactivation by penicillins were decreased 30-50-fold, whereas the reactions with cephalosporins were even more affected. The efficiency of hydrolysis against the peptide substrate was also seriously decreased. More surprisingly, the mutant was completely unable to catalyse transpeptidation reactions. The conservation of an hydroxylated residue in this position in PBPs is thus easily explained by these results.

Purification, properties, and kinetics of enzymatic acylation with beta-lactams of soluble penicillin-binding protein 2a. A major factor in methicillin-resistant Staphylococcus aureus

Intrinsic resistance toward beta-lactams in methicillin-resistant Staphylococcus aureus strains, a major source of nosocomial infections, is believed to be caused mainly by penicillin-binding protein 2a (PBP2a). This protein resembles other penicillin-binding proteins that are involved in bacterial cell wall biosynthesis and are the targets of active site acylation by beta-lactam antibiotics. PBP2a, however, presumably remains active at therapeutic concentrations of beta-lactams. In this paper, we describe a three-step purification of a soluble form of PBP2a (PBP2a') to apparent homogeneity using anion-and cation-exchange, and dye-ligand affinity chromatographies. Purified PBP2a' was a 74-kDa monomeric protein that appeared to be folded. The protein was evaluated for its enzymatic acylation with beta-lactams initially by fluorescence quenching and then kinetically by radioactive labeling. Using a modified 125I-labeled penicillin V-acylation assay, the apparent Km of PBP2a' for penicillin V was 1.2 mM. Three other beta-lactams, each of which exhibited significant fluorescence quenching, acted as strong competitive inhibitors of penicillin V with apparent Ki values of 123.4, 36.1, and 12.4 microM, respectively. By a new beta-lactam preincubation analysis, these compounds could function as substrates with similar Km values. Also, the acylation rates of different beta-lactams could be readily ascertained. The enzymatic acylation data substantiate the major causative role of PBP2a in the bacterial resistance. The quantitative radioactive acylation assays are potentially useful in screening for a potent inhibitor of the enzyme.

Binding site-shaped repeated sequences of bacterial wall peptidoglycan hydrolases

The non-catalytic C-terminal regions of the N-acetylmuramidase (lysozyme) of Clostridium acetobutylicum and N-acetylmuramoyl(D-lactyl)-L-alanine amidases CwlA of Bacillus subtilis, ORFL3 and CwlL of Bacillus licheniformis were previously reported to have similarities with the amino acid sequence of the non-catalytic N-terminal module of the Streptomyces albus G Zn DD-peptidase. This peptidase is a bipartite protein of known three-dimensional structure. Its non-catalytic N-terminal module possesses, exposed at the surface, an elongated crevice which is defined by a loop-helix-loop-helix motif that consists of two repeats, each 16 amino acid residues long, connected by a heptapeptide and whose design is compatible with its possible functioning as a substrate recognition and binding site. Amino acid alignments suggest that cavities nearly identical in shape to that present in the non-catalytic module of the S. albus peptidase, are borne by the C-terminal regions of the CwlA amidase (in one copy), the lysozyme and the ORFL3 and CwlL amidases (in two copies). Since a common feature of the five enzymes is their substrate, the bacterial cell wall peptidoglycan, we interpret the striking similarity of their non-catalytic N- or C-terminal modules to suggest that these modules are involved in the binding of these exocellular enzymes to their insoluble wall substrate.

Analysis of the membrane-anchoring properties of the putative amphiphilic alpha-helical anchor at the C-terminus of Escherichia coli PBP 6

Penicillin-binding protein (PBP) 6 is anchored to the periplasmic face of the Escherichia coli inner membrane. Analysis of the C-terminal 20 amino acids of PBP 6 implies the presence of a C-terminal amphiphilic alpha-helical anchor comparable to that of PBP 5. A C-terminal deletion of PBP 6 was constructed; it resulted in the release of the protein from the inner membrane into the periplasm, thus confirming that this region is essential for anchoring. Treatment of E. coli K12 membrane vesicles with various reagents was used to probe the membrane-binding characteristics of both PBP 5 and PBP 6. The results indicate that, although the strength of membrane anchoring of PBP 6 is weaker than that of PBP 5, both modes of anchoring involve a large hydrophobic element and have similar membrane-binding characteristics. This is in agreement with the hypothesis that both proteins exhibit the same novel method of anchoring.

Alterations of murein structure and of penicillin-binding proteins in minicells from Escherichia coli

Minicells, as compared with a whole cell preparation of a minA/B mutant of Escherichia coli, showed a number of changes in the structure of the murein sacculus. Minicell murein was enriched in LD-A2pm-A2pm crossbridges by about 66% and reduced in the amount of L-Ala-D-Glu dipeptide moieties by about 55%. In addition, the length distribution of the glycan strands in the murein was shifted to shorter lengths. In particular, the relative amount of the shortest possible strand, the size of a disaccharide, was more than doubled. Minicells were also found to have an altered penicillin-binding protein (PBP) pattern. Whereas PBP4 and PBP6 were greatly diminished, PBP8 was significantly increased. We consider it unlikely that the sort of changes observed in murein structure reflect the fact that minicells are composed of two hemispherical polar caps.

The dacA gene of Bacillus stearothermophilus coding for D-alanine carboxypeptidase: cloning, structure and expression in Escherichia coli and Pichia pastoris

The bacterial D-alanine carboxypeptidases (CPases) remove C-terminal D-alanyl residues from sugar-peptide cell wall precursors. The CPases have many characteristics in common with the high-M(r) penicillin-binding proteins (PBPs) whose inhibition by beta-lactam antibiotics is lethal. The CPases are attractive as model PBPs, because of their relatively lower M(r) and higher activity in vitro. We have cloned and sequenced the Bacillus stearothermophilus gene (dacA) coding for a membrane-bound CPase. The nucleotide (nt) sequence of the gene is homologous to that of the Escherichia coli and Bacillus subtilis dacA loci, which also code for membrane-bound CPases. E. coli host cells lysed when expression of B. stearothermophilus dacA was induced. The same coding sequence was expressed in the methylotrophic yeast, Pichia pastoris, using the alcohol oxidase-1 (AOX1) promoter. Over 100 micrograms/ml of CPase was efficiently secreted into the medium after induction by methanol, without adversely affecting this host. The yeast product is indistinguishable from the native enzyme in structure and activity. The ability to secrete large amounts of heterologous protein and the lack of endogenous peptidoglycan metabolism makes P. pastoris an attractive candidate for the production of PBPs.

Crystallization of a genetically engineered water-soluble primary penicillin target enzyme. The high molecular mass PBP2x of Streptococcus pneumoniae

A genetically engineered water-soluble derivative of PBP2x of Streptococcus pneumoniae has been produced, purified and crystallized in a form suitable for X-ray diffraction analysis. The best crystals have been grown at 15 degrees C, from solutions containing 8% polyethylene glycol 10,000 at pH values ranging from 3.9 to 6.0. These crystals diffract to a resolution of 3.5 A and have a space group P6(1)22 (or enantiomorph) with unit cell dimensions of a = b = 162.2 A, c = 171.8 A, alpha = beta = 90 degrees, gamma = 120 degrees. The molecular mass and cell dimensions suggest that there is one molecule of enzyme per asymmetric unit. The breakdown of a chromogenic cephalosporin derivative diffused into a crystal reveals clearly that the enzyme is active in the crystalline state.

The mechanism of action of DD-peptidases: the role of tyrosine-159 in the Streptomyces R61 DD-peptidase

Tyrosine-159 of the Streptomyces R61 penicillin-sensitive DD-peptidase was replaced by serine or phenylalanine. The second mutation yielded a very poorly active protein whose rate of penicillin binding was also drastically decreased, except for the reactions with nitrocefin and methicillin. The consequences of the first mutation were more surprising, since a large proportion of the thiolesterase activity was retained, together with the penicillin-binding capacity. Conversely, the peptidase properties was severely affected. In both cases, a drastic decrease in the transferase activity was observed. The results are compared with those obtained by mutation of the corresponding residue in the class A beta-lactamase of Streptomyces albus G.

Domain organization of penicillin-binding protein 5 from Escherichia coli analysed by C-terminal truncation

The structural organization of penicillin-binding protein (PBP) 5 was investigated by C-terminal truncation. Compared with other low-M(r) penicillin-interacting proteins, PBP5 carries a C-terminal extension of about 100 amino acids. The sites for introduction of stop codons were chosen on the basis of the established three-dimensional structure of the Streptomyces albus G beta-lactamase [Dideberg, Charlier, Wéry, Dehottay, Dusart, Erpicum, Frère and Ghuysen (1987) Biochem. J. 245, 911-913] and comparative hydrophobic cluster analysis [Gaboriaud, Bissery, Bencheritt and Mornon (1987) FEBS Lett. 224, 149-155]. Two stop codons were introduced at positions Ile-354 or Val-348 to construct an optimized soluble form of PBP5 for crystallization purposes. The newly constructed soluble and enzymically active form (PBP5s353) was isolated by dye-affinity chromatography and gave rise to small crystals. Another two stop codons were introduced at positions Arg-261 or Ala-276 to determine the minimal enzymically active 'core protein'. The truncated form (PBP5s275), missing the entire C-terminal extension, showed unaltered penicillin-binding characteristics and a catalytic-centre activity 40% that of PBP5s353 + 9 using bisacetyl-L-Lys-D-Ala-D-Ala as substrate. This protein, however was more susceptible to proteolytic degradation, which might indicate a role of the C-terminal portion in stabilizing the protein.

Primary and predicted secondary structures of the Actinomadura R39 extracellular DD-peptidase, a penicillin-binding protein (PBP) related to the Escherichia coli PBP4

As derived from gene cloning and sequencing, the 489-amino-acid DD-peptidase/penicillin-binding protein (PBP) produced by Actinomadura R39 has a primary structure very similar to that of the Escherichia coli PBP4 [Mottl, Terpstra & Keck (1991) FEMS Microbiol. Lett. 78, 213-220]. Hydrophobic-cluster analysis of the two proteins shows that, providing that a large 174-amino-acid stretch is excluded from the analysis, the bulk of the two polypeptide chains possesses homologues of the active-site motifs and secondary structures found in the class A beta-lactamase of Streptomyces albus G of known three-dimensional structure. The 174-amino-acid insert occurs at equivalent places in the two PBPs, between helices alpha 2 and alpha 3, away from the active site. Such an insert is unique among the penicilloyl serine transferases. It is proposed that the Actinomadura R39 PBP and E. coli PBP4 form a special class, class C, of low-Mr PBPs/DD-peptidases. A vector has been constructed and introduced by electrotransformation in the original Actinomadura R39 strain, allowing high-level expression and secretion of the DD-peptidase/PBP (250 mg.l-1). The gene encoding the desired protein is processed differently in Actinomadura R39 and Streptomyces lividans. Incorrect processing in Streptomyces lividans leads to a secreted protein which is inert in terms of DD-peptidase activity and penicillin-binding capacity.

Structural similarity of D-aminopeptidase to carboxypeptidase DD and beta-lactamases

The gene for D-aminopeptidase (dap) has been isolated from the bacterium Ochrobactrum anthropi SCRC C1-38 [Asano, Y., Nakazawa, A., Kato, Y., & Kondo, K. (1989) J. Biol. Chem. 264, 14233-14239] and its nucleotide sequence determined. An expression plasmid pC138DP (4.5 kb) was constructed by placing the gene downstream of the lac promoter of pUC19. The amount of the enzyme in the cell-free extract of Escherichia coli JM109/pC138DP was elevated to 288,000 units/L of culture, which is about 3600-fold over that of O. anthropi SCRC C1-38. The enzyme comprised about 30% of the total extractable cellular protein. The gene consisted of an open reading frame of 1560 nucleotides which specifies a protein of Mr 57,257. The deduced amino acid sequence of the enzyme showed that it is related to carboxypeptidase DD, beta-lactamases, and penicillin-binding proteins. Seven mutants of the enzyme were generated by site-specific mutagenesis to explore the roles of the residues of interest, around the sequence Ser61-Xaa-Xaa-Lys64, where Xaa is any amino acid, since the identical sequences also appear in the penicillin-recognizing peptide hydrolases with Ser at the active sites. The mutant enzymes expressed in E. coli were purified to homogeneity and kinetically characterized. Replacements of the site at Ser61 and Lys64 yielded mutants showing significantly reduced Vmax values, while most of the Km values remained unchanged. Changes at Cys60, which is adjacent to the likely active center Ser61, to Ser and Gly resulted in the production of enzyme less sensitive to PCMB, with almost unaltered Vmax/Km values. The enzyme appears to be a serine peptidase rather than a thiol one. The inhibition by PCMB in the wild-type enzyme may have been caused by a formation of a mercaptide bond between Cys 60 and PCMB. Considering that D-aminopeptidase, carboxypeptidase DD (a penicillin-binding protein), and beta-lactamase have a common feature in recognizing peptides containing D-amino acid and that the former two catalyze transpeptidation reactions with substrates containing D-alanyl-D-alanine moieties, we propose that the enzyme is a new member of the "penicillin-recognizing enzymes". We showed that the enzyme is actually inhibited by beta-lactam compounds, such as 6-APA, 7-ACA, benzylpenicillin, and ampicillin, although they are not the substrate for the enzyme. The relationship between the primary structures and the reactions catalyzed by D-aminopeptidase and other serine hydrolases beta-lactamases and carboxypeptidase DD is discussed.(ABSTRACT TRUNCATED AT 400 WORDS)

Relatedness of penicillin-binding proteins from various Listeria species

The heterogeneity of penicillin-binding proteins (PBPs) of five Listeria species was investigated. Similarities in the overall PBP pattern were found between those of L. welshimeri and L. innocua, and between L. ivanovii and L. seeligeri, and all were distinct from the PBPs of L. monocytogenes. In all species, however, the primary target for beta-lactam antibiotics, as identified in L. monocytogenes recently, appeared highly conserved. In addition, the low-Mr PBP 5 was biochemically very similar in all strains and contained identical binding properties to beta-lactam compounds, suggesting that this protein may play an important role. All other PBPs varied considerably in their penicilloyl-peptide pattern, indicating differences in their amino acid sequences.

Mode of membrane insertion and sequence of a 32-amino acid peptide stretch of the penicillin-binding protein 4 of Enterococcus hirae

Analysis of water-soluble derivatives of the Enterococcus hirae 75-kDa membrane-bound penicillin-binding protein 4 (PBP4) has yielded the amino acid sequence of a 32-amino acid polypeptide stretch. This peptide is similar to peptide segments known to occur in the N-terminal domain of high-Mr PBPs of class B. The E. hirae PBP4 probably belongs to the same class. It is anchored in the membrane at the N-terminus of the polypeptide chain.

Effect of a beta-lactamase inhibitor, tazobactam, on growth and penicillin-binding proteins of Borrelia burgdorferi

The effects of tazobactam, a relatively new beta-lactamase inhibitor, were investigated on growth and penicillin-binding proteins (PBPs) of Borrellia burgdorferi. A previous communication from our group demonstrated several proteins capable of binding labelled penicillin in this organism. Of these proteins, 94-kDa and 57-kDa PBPs possessed the highest affinity for penicillin and were assumed to be essential proteins involved in cell-wall synthesis. In these experiments, tazobactam was used in competition binding experiments as well as on whole spirochetes. Only the 94-kDa and 57-kDa PBPs were affected by increasing amounts of tazobactam during competition-binding experiments and growth of B. burgdorferi was also inhibited. These results may explain the in vitro activity of beta-lactamase inhibitors in general and suggest a utility for these compounds when examining PBPs with hydrolysing activity and/or organisms with beta-lactamases.

Penicillin-binding proteins in Streptococcus pneumoniae: alterations during development of intrinsic penicillin resistance

Four out of the five high molecular weight penicillin-binding proteins (PBPs) of Streptococcus pneumoniae are involved in the development of intrinsic penicillin resistance. In beta-lactam resistant laboratory mutants, point mutations in the PBP 2x-genes were identified that result in low penicillin-affinity mutant proteins. In contrast, PBPs 1a, 2x, and 2b of resistant clinical isolates are highly altered as can be recognized biochemically and immunologically; DNA sequence analysis of the PBP 2x gene from resistant strains confirmed these results. The variability of the three PBPs analyzed implies a very heterogeneous gene pool accessible to the pneumococcus that is used for recruitment of resistant PBP genes in wild type strains.

Penicillin-binding protein 4 of Escherichia coli shows a novel type of primary structure among penicillin-interacting proteins

The nucleotide sequence of a 1884 bp DNA fragment of E. coli, carrying the gene dacB, was determined. The DNA codes for penicillin-binding protein 4 (PBP4), an enzyme of 477 amino acids, being involved as a DD-carboxypeptidase-endopeptidase in murein metabolism. The enzyme is translated with a cleavable signal peptide of 20 amino acids, which was verified by sequencing the amino-terminus of the isolated protein. The characteristic active-site fingerprints SXXK, SXN and KTG of class A beta-lactamases and penicillin-binding proteins were located in the sequence. On the basis of amino acid alignments we propose, that PBP4 and class A beta-lactamases share a common evolutionary origin but PBP4 has acquired an additional domain of 188 amino acids in the region between the SXXK and SXN elements.

Imipenem resistance in Acinetobacter baumanii is due to altered penicillin-binding proteins

The comparison of a clinical Acinetobacter baumanii isolate (strain No. 4852/88) and its selected imipenem-resistant (IMR) clone exhibited a complex reorganization of the penicillin-binding proteins (PBPs) with diminished labelling of all PBPs except the 24-kD PBP which showed an increased binding of 14C-penicillin. This protein could not be saturated by preincubation of membranes with imipenem at 8-fold the MIC of imipenem, thus indicating PBP alterations responsible for imipenem resistance. In A. baumanii 4852/88 seven PBPs with the apparent molecular weights of 94, 84, 65, 61, 48, 40 and 24 kD could be detected. beta-Lactamase production was barely detectable in any case and could not be enhanced in the presence of various beta-lactams as the inducer. The outer membrane proteins were found identical in both the wild-type strain and the Im clone. So far, imipenem-resistant A. baumanii isolates have been isolated twice in our diagnostic laboratory; however, no implications on the future relevance of the above findings can be made.