Nucleotide sequences of the penicillin-binding protein 5 and 6 genes of<i>Escherichia coli</i>

Broome-Smith, Jenny K.; Ioannidis, Ioannis; Edelman, A.; Spratt, Brian G.

doi:10.1093/nar/16.4.1617

Cited by 62 publications

(28 citation statements)

References 4 publications

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“…The low homology (17%) with PBP 4 was expected, since this PBP shows poor homology with all other PBPs (30). However, even 30% is a relatively low level of overall identity when one considers that PBPs 5 and 6 from E. coli, both of which are low-molecular-weight PBPs with D,D-carboxypeptidase activity, are 63% identical to one another (5). Nevertheless, these results are consistent with the fact that polyclonal antibodies raised against PBP 5* did not detectably cross-react with any other PBP.…”

Section: Subtilis Was A-i-d-v-s-a-k-x-a-i-i-i-d-g-g-a-s-g This Sequementioning

confidence: 94%

Isolation and sequence analysis of dacB, which encodes a sporulation-specific penicillin-binding protein in Bacillus subtilis

Buchanan

Ling

1992

J Bacteriol

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A novel penicillin-binding protein (PBP 5*) with D,D-carboxypeptidase activity is synthesized by Bacilus subtilis, beginning at about stage m of sporulation. The complete gene (dacB) for this protein was cloned by immunoscreening of an expression vector library and then sequenced. The identity of dacB was verified not only by the size and cross-reactivity of its product but also by the presence of the nucleotide sequence that coded for the independently determined NH2 terminus of PBP 5*. Analysis of its complete amino acid sequence confirmed the hypothesis that this PBP is related to other active-site serine D,D-peptidases involved in bacterial cell wall metabolism. PBP 5* had the active-site domains common to all PBPs, as well as a cleavable amino-terminal signal peptide and a carboxy-terminal membrane anchor that are typical features of low-molecular-weight PBPs. Mature PBP 5* was 355 amino acids long, and its mass was calculated to be 40,057 daltons. What is unique about this PBP is that it is developmentally regulated. Analysis of the sequence provided support for the hypothesis that the sporulation specificity and mother cell-specific expression of dacB can be attributed to recognition of the gene by a sporulation-specific sigma factor. There was a good match of the putative promoter of dacB with the sequence recognized by sigma factor E (oE), the subunit of RNA polymerase that is responsible for early mother cell-specific gene expression during sporulation. Analysis of PBP 5* production by various spo mutants also suggested that dacB expression is on a oE-dependent pathway.The penicillin-binding proteins (PBPs) are a family of membrane-bound enzymes that are active in the metabolism of prokaryotic cell walls (16). They are evolutionarily related to some of the soluble P-lactamases and D,D-peptidases secreted by bacteria and also have some structural features in common with a penicillin-binding transmembrane protein involved in signal transduction (24,46,62). The active-site serine of all of these penicillin-interactive proteins is part of the conserved domain S-X-X-K, which is located near the amino terminus of the 1-lactamases and the mature form of those PBPs with a molecular mass of less than 50 kDa but more towards the middle of the sequence in the larger PBPs (24). Closer to the carboxy terminus, all of these proteins also have the sequence K-T-G, H-T-G, or K-S-G, which is an essential part of the tertiary structure of the active site (24). The class A ,-lactamases and the PBPs also have a third domain (S-X-N) in common, which is located between the other two (46).Our studies have focused on PBP 5*, which is different from all of the other PBPs described so far because it is developmentally regulated. This protein, which has D,Dcarboxypeptidase activity in vitro, is not synthesized by Bacillus subtilis until about stage III of sporulation (43,49,50). Although it has a lower molecular weight than any of the six vegetative PBPs in this species, it is not a derivative of one of them (10, 50). Its locatio...

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Section: Subtilis Was A-i-d-v-s-a-k-x-a-i-i-i-d-g-g-a-s-g This Sequementioning

confidence: 94%

Isolation and sequence analysis of dacB, which encodes a sporulation-specific penicillin-binding protein in Bacillus subtilis

Buchanan

Ling

1992

J Bacteriol

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“…As the major PBP of E. coli (60,243), PBP5 has been extensively studied (72,205,280,301). It was identified with D-alanine carboxypeptidase IA activity encoded by the dacA gene (30,166,191,242). Its primary structure shows sequence similarity with PBP4, PBP6, and ␤-lactamases (30,163).…”

Section: Penicillin-binding Peptidasesmentioning

confidence: 99%

“…It was identified with D-alanine carboxypeptidase IA activity encoded by the dacA gene (30,166,191,242). Its primary structure shows sequence similarity with PBP4, PBP6, and ␤-lactamases (30,163). Synthesized by the removal of a hydrophobic N-terminal signal sequence, PBP5 localizes in the cytoplasmic membrane, with the bulk of the protein extending into the periplasm (208,209).…”

Section: Penicillin-binding Peptidasesmentioning

confidence: 99%

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Peptidoglycan Hydrolases of Escherichia coli

Heijenoort

2011

Microbiol Mol Biol Rev

190

233

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SUMMARY The review summarizes the abundant information on the 35 identified peptidoglycan (PG) hydrolases of Escherichia coli classified into 12 distinct families, including mainly glycosidases, peptidases, and amidases. An attempt is also made to critically assess their functions in PG maturation, turnover, elongation, septation, and recycling as well as in cell autolysis. There is at least one hydrolytic activity for each bond linking PG components, and most hydrolase genes were identified. Few hydrolases appear to be individually essential. The crystal structures and reaction mechanisms of certain hydrolases having defined functions were investigated. However, our knowledge of the biochemical properties of most hydrolases still remains fragmentary, and that of their cellular functions remains elusive. Owing to redundancy, PG hydrolases far outnumber the enzymes of PG biosynthesis. The presence of the two sets of enzymes acting on the PG bonds raises the question of their functional correlations. It is difficult to understand why E. coli keeps such a large set of PG hydrolases. The subtle differences in substrate specificities between the isoenzymes of each family certainly reflect a variety of as-yet-unidentified physiological functions. Their study will be a far more difficult challenge than that of the steps of the PG biosynthesis pathway.

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“…Gene cloning and sequencing has yielded the amino acid sequence of the protein. Pair-wise comparison with the other low-M, PBPs of known primary structure has led to the conclusion that (1) the Streptomyces K15 PBP, the Escherichia coli PBPs 5 and 6 (Broome-Smith et al, 1988), the Bacillus subtilis PBP5 (Todd et al, 1986) and the spollA product, which is thought to be a PBP specifically involved in sporulation (Wu & Piggot, 1991), belong to a same class A of low-M, PBPs/DDpeptidases, and (2) these PBPs adopt a polypeptide scaffolding comparable with that of the class A fl-lactamases of Staphylococcus aureus (Herzberg & Moult, 1987) and Streptomyces albus G (Dideberg et al, 1987;Lamotte-Brasseur et al, 1991).…”

Section: Introductionmentioning

confidence: 99%

Amino acid sequence of the penicillin-binding protein/dd-peptidase of Streptomyces K15. Predicted secondary structures of the low Mr penicillin-binding proteins of class A

Palomeque-Messia

Englebert

Leyh‐Bouille

et al. 1991

Biochemical Journal

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The low-Mr penicillin-binding protein (PBP)/DD-transpeptidase of Streptomyces K15 is synthesized in the form of a 291-amino acid-residue precursor possessing a cleavable 29-amino acid-residue signal peptide. Sequence-similarity searches and hydrophobic-cluster analysis show that the Streptomyces K15 enzyme, the Escherichia coli PBPs/DD-carboxypeptidases 5 and 6, the Bacillus subtilis PBP/DD-carboxypeptidase 5 and the spollA product (a putative PBP involved in the sporulation of B. subtilis) are structurally related and form a distinct class A of low-M, PBPs/DD-peptidases. The distribution of the hydrophobic clusters along the amino acid sequences also shows that the Streptomyces K15 PBP, and by extension the other PBPs of class A, have similarity in the polypeptide folding, with the ,8-lactamases of class A, with as reference the Streptomyces albus G and Staphylococcus aureus ,J-lactamases of known three-dimensional structure. This comparison allows one to predict most of the secondary structures in the PBPs and the amino acid motifs that define the enzyme active sites.

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Nucleotide sequences of the penicillin-binding protein 5 and 6 genes ofEscherichia coli

Abstract: Accession nos. dacA=X06479 and dacC=X06480 Penicillin-binding proteins (PBPs) 5 and 6 are the major D-alanine carboxypeptidases of Escherichia coli. The PBP 5 and PBP 6 genes (dacA and dacC respectively) have been cloned 1T2and the nucleotide sequence of a 1597

Cited by 62 publications

References 4 publications

Isolation and sequence analysis of dacB, which encodes a sporulation-specific penicillin-binding protein in Bacillus subtilis

Isolation and sequence analysis of dacB, which encodes a sporulation-specific penicillin-binding protein in Bacillus subtilis

Peptidoglycan Hydrolases of Escherichia coli

Amino acid sequence of the penicillin-binding protein/dd-peptidase of Streptomyces K15. Predicted secondary structures of the low Mr penicillin-binding proteins of class A

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