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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.
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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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