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    dacA D-alanyl-D-alanine carboxypeptidase DacA [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 945222, updated on 17-Dec-2024

    Summary

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    Official Symbol
    dacA
    Official Full Name
    D-alanyl-D-alanine carboxypeptidase DacA
    Primary source
    ECOCYC:EG10201
    Locus tag
    b0632
    See related
    ASAP:ABE-0002168
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    ECK0625; pfv
    Summary
    A dacA deletion suppresses ftsK (Ts). [More information is available at EcoGene: EG10201]. D-alanyl-D-alanine carboxypeptidase IA (PBP5) is a penicillin-sensitive, membrane-bound enzyme required for trimming the carboxy-terminal D-alanyl residues from peptidoglycan pentapeptides. -lactam antibiotics act by binding covalently to PBPs resulting in their deactivation and ultimately leading to cell death. [More information is available at EcoCyc: EG10201].
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    Genomic context

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    Sequence:
    NC_000913.3 (662752..663963, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene lipoyl(octanoyl) transferase Neighboring gene DUF493 domain-containing protein YbeD Neighboring gene rare lipoprotein RlpA Neighboring gene peptidoglycan glycosyltransferase MrdB

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. A study on the C-terminal membrane anchoring of Escherichia coli penicillin-binding protein 5. Brandenburg K, et al. Biochem Biophys Res Commun, 2002 Jan 11. PMID 11779187
    2. A large displacement of the SXN motif of Cys115-modified penicillin-binding protein 5 from Escherichia coli. Nicola G, et al. Biochem J, 2005 Nov 15. PMID 16038617, Free PMC Article
    3. Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor: a role for Ser-110 in deacylation. Nicola G, et al. Biochemistry, 2005 Jun 14. PMID 15938610
    4. Properties and crystallization of a genetically engineered, water-soluble derivative of penicillin-binding protein 5 of Escherichia coli K12. Ferreira LC, et al. Eur J Biochem, 1988 Jan 15. PMID 3276513
    5. Site-directed mutants of a soluble form of penicillin-binding protein 5 from Escherichia coli and their catalytic properties. Nicholas RA, et al. J Biol Chem, 1988 Feb 5. PMID 3276680

    See all (105) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study reports the structure of a E.coli PBP5-meropenem acyl enzyme complex in order to completely describe the molecular interactions which facilitate meropenem inhibition of the YcbB and PBP5 partners. Results provide structural insight into D,D-transpeptidase bypass in E. coli and structural insight into the role of L,D-transpeptidation of PG in Gram negative bacteria.
      Title: Structural insight into YcbB-mediated beta-lactam resistance in Escherichia coli.
    2. Studied alanine substitution with glutamic acid at Position 184 in Escherichia coli D-alanyl-D-alanine carboxypeptidase (PBP5); results found substitution of A184 to E of Omega-like loop alone can introduce cephalosporinase activity in E. coli PBP5.
      Title: Substitution of Alanine at Position 184 with Glutamic Acid in Escherichia coli PBP5 Ω-Like Loop Introduces a Moderate Cephalosporinase Activity.
    3. Authors infer that biochemically DacD and PBP5 are more closely related to each other than to PBP6, enabling DacD and PBP5 to play a nearly similar physiological function in terms of recovering the lost beta-lactam resistance.
      Title: Moderate deacylation efficiency of DacD explains its ability to partially restore beta-lactam resistance in Escherichia coli PBP5 mutant.
    4. The present report shows that BolA is a transcriptional regulator of the dacA and dacC genes, thus regulating both DD-carboxypeptidases PBP5 and PBP6 and thereby demonstrating the versatility of BolA as a cellular regulator.
      Title: BolA affects cell growth, and binds to the promoters of penicillin-binding proteins 5 and 6 and regulates their expression.
    5. Results indicating a change in the active-site microarchitectures of PBP5 and 6 as a plausible cause of the difference in their biochemical behaviors.
      Title: Differences in active-site microarchitecture explain the dissimilar behaviors of PBP5 and 6 in Escherichia coli.
    6. Reversion to beta-lactam resistance was observed in the mutants upon complementing with cloned PBP5, indicating the involvement of PBP5 in maintaining an O-antigen-independent intrinsic beta-lactam resistance in E. coli cells.
      Title: Deletion of penicillin-binding protein 5 (PBP5) sensitises Escherichia coli cells to beta-lactam agents.
    7. The roles of the residues Lys47 and Lys213 in the catalytic machinery of PBP 5 was explored. The pH dependence of kcat/Km and of kcat for the wild-type PBP 5 and for the two gamma-thialysine mutant variants at positions 47 and 213 were evaluated.
      Title: Catalytic mechanism of penicillin-binding protein 5 of Escherichia coli.
    8. N-terminus verified by Edman degradation on mature peptide
      Title: Amino acid sequence homologies between Escherichia coli penicillin-binding protein 5 and class A beta-lactamases.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables beta-lactamase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables beta-lactamase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables beta-lactamase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables carboxypeptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables carboxypeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables carboxypeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables penicillin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables serine-type D-Ala-D-Ala carboxypeptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables serine-type D-Ala-D-Ala carboxypeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables serine-type D-Ala-D-Ala carboxypeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell division EXP
    Inferred from Experiment
    more info
    		 PubMed 
    involved_in cell wall organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in peptidoglycan biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within peptidoglycan metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of cell shape EXP
    Inferred from Experiment
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of cell shape IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell shape IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of cell shape IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of cell shape IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in outer membrane-bounded periplasmic space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    D-alanyl-D-alanine carboxypeptidase DacA
    NP_415165.1

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      662752..663963 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_415165.1 D-alanyl-D-alanine carboxypeptidase DacA [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_415165.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A0A0GRC5, A0A1X3JKK6, A0A8E0KSK6, W1EXD7
      Conserved Domains (1) summary
      PRK10793
      Location:1 → 403
      PRK10793; D-alanyl-D-alanine carboxypeptidase fraction A; Provisional
    Nucleotide Protein
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