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    ldtD L,D-transpeptidase LdtD [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 945541, updated on 3-Dec-2024

    Summary

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    Official Symbol
    ldtD
    Official Full Name
    L,D-transpeptidase LdtD
    Primary source
    ECOCYC:EG11253
    Locus tag
    b0925
    See related
    ASAP:ABE-0003142
    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
    ECK0916; ycbB
    Summary
    YcbB catalyzes the rare meso-DAP(3)-->meso-DAP(3) murein cross-links (Magnet, 2008).The first 30 aa are predicted to be a type I signal peptide. [More information is available at EcoGene: EG11253]. YcbB is an L,D-transpeptidase responsible removal of the D-alanine residue of an acyl donor peptidoglycan tetrapeptide stem and attachment of the meso-diaminopimelyl (DAP) residue to the meso-DAP residue of a second, acyl acceptor peptidoglycan tetrapeptide. [More information is available at EcoCyc: EG11253].
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    Genomic context

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    Sequence:
    NC_000913.3 (981047..982894)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene tRNA cmo(5)U34 methyltransferase Neighboring gene chromosome partitioning protein MukF Neighboring gene chromosome partitioning protein MukE Neighboring gene chromosome partitioning protein MukB Neighboring gene peptidoglycan L,D-endopeptidase Neighboring gene hydroxyacylglutathione hydrolase GloC

    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. The new gene mukB codes for a 177 kd protein with coiled-coil domains involved in chromosome partitioning of E. coli. Niki H, et al. EMBO J, 1991 Jan. PMID 1989883, Free PMC Article
    2. The Cpx envelope stress response modifies peptidoglycan cross-linking via the L,D-transpeptidase LdtD and the novel protein YgaU. Bernal-Cabas M, et al. J Bacteriol, 2015 Feb. PMID 25422305, Free PMC Article
    3. Rapid acid treatment of Escherichia coli: transcriptomic response and recovery. Kannan G, et al. BMC Microbiol, 2008 Feb 26. PMID 18302792, Free PMC Article
    4. Identification of the L,D-transpeptidases for peptidoglycan cross-linking in Escherichia coli. Magnet S, et al. J Bacteriol, 2008 Jul. PMID 18456808, Free PMC Article
    5. BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. Berven FS, et al. Nucleic Acids Res, 2004 Jul 1. PMID 15215418, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Authors show that the activation of the Cpx response causes an increase in the abundance of diaminopimelic acid (DAP)-DAP cross-links that involves LdtD and YgaU.
      Title: The Cpx envelope stress response modifies peptidoglycan cross-linking via the L,D-transpeptidase LdtD and the novel protein YgaU.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Homology

    General protein information

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    Preferred Names
    L,D-transpeptidase LdtD

    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
      981047..982894
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_415445.1 L,D-transpeptidase LdtD [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_415445.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8S7JW60
      Conserved Domains (1) summary
      PRK10594
      Location:1 → 615
      PRK10594; murein L,D-transpeptidase; Provisional
    Nucleotide Protein
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