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    dacB peptidoglycan DD-endopeptidase DacB [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947693, updated on 3-Dec-2024

    Summary

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    Official Symbol
    dacB
    Official Full Name
    peptidoglycan DD-endopeptidase DacB
    Primary source
    ECOCYC:EG10202
    Locus tag
    b3182
    See related
    ASAP:ABE-0010458
    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
    ECK3171
    Summary
    False positive lipoprotein prediction, verified SPI substrate. [More information is available at EcoGene: EG10202]. PBP4 is a penicillin-sensitive protein that catalyzes both D-alanyl-D-alanine carboxypeptidase and D-alanyl-D-alanine endopeptidase activities, though the former has been shown to occur at low levels. [More information is available at EcoCyc: EG10202].
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    Genomic context

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    Sequence:
    NC_000913.3 (3328963..3330396)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene ribosome assembly factor YhbY Neighboring gene transcription elongation factor GreA Neighboring gene GTPase ObgE Neighboring gene putative transporter YhbE

    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. Simultaneous deletion of D-alanine carboxypeptidase IB-C and penicillin-binding component IV in a mutant of Escherichia coli K12. Iwaya M, et al. Proc Natl Acad Sci U S A, 1977 Jul. PMID 331323, Free PMC Article
    2. Mutants of Escherichia coli lacking in highly penicillin-sensitive D-alanine carboxypeptidase activity. Matsuhashi M, et al. Proc Natl Acad Sci U S A, 1977 Jul. PMID 331322, Free PMC Article
    3. Purification and light-scattering analysis of penicillin-binding protein 4 from Escherichia coli. Fusetti F, et al. Microb Drug Resist, 1996 Spring. PMID 9158725
    4. Multiple mechanisms of membrane anchoring of Escherichia coli penicillin-binding proteins. Gittins JR, et al. FEMS Microbiol Rev, 1994 Jan. PMID 8117464
    5. Purification, crystallisation and preliminary X-ray analysis of penicillin binding protein 4 from Escherichia coli, a protein related to class A beta-lactamases. Thunnissen MM, et al. J Mol Biol, 1995 Mar 24. PMID 7707365

    See all (86) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mutational analysis of the substrate specificity of Escherichia coli penicillin binding protein 4.
      Title: Mutational analysis of the substrate specificity of Escherichia coli penicillin binding protein 4.
    2. N-terminus verified by Edman degradation on mature peptide
      Title: Penicillin-binding protein 4 of Escherichia coli shows a novel type of primary structure among penicillin-interacting proteins.
    3. The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented
      Title: Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics.
    4. auxiliary role in maintenance of normal rod shape of E coli
      Title: Endopeptidase penicillin-binding proteins 4 and 7 play auxiliary roles in determining uniform morphology of Escherichia coli.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables carboxypeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables penicillin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    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 
    enables serine-type carboxypeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables serine-type carboxypeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables serine-type carboxypeptidase activity ISM
    Inferred from Sequence Model
    more info
    		 PubMed 
    enables serine-type endopeptidase activity ISM
    Inferred from Sequence Model
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within FtsZ-dependent cytokinesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell wall organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in peptidoglycan biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in peptidoglycan metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within peptidoglycan metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell shape IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to antibiotic IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in periplasmic space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in periplasmic space IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    peptidoglycan DD-endopeptidase DacB

    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
      3328963..3330396
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417649.1 peptidoglycan DD-endopeptidase DacB [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417649.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A3P5DUN5, A0A8S7TGN9
      Conserved Domains (1) summary
      PRK11113
      Location:1 → 477
      PRK11113; D-alanyl-D-alanine carboxypeptidase/endopeptidase; Provisional
    Nucleotide Protein
    Heading Accession and Version

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