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

Gene ID: 945222, updated on 6-Oct-2023

Summary

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Gene symbol
dacA
Gene description
D-alanyl-D-alanine carboxypeptidase DacA
Primary source
ASAP:ABE-0002168
Locus tag
b0632
See related
ECOCYC:EG10201
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. Substitution of Alanine at Position 184 with Glutamic Acid in Escherichia coli PBP5 Ω-Like Loop Introduces a Moderate Cephalosporinase Activity. Kar D, et al. Protein J, 2018 Apr. PMID 29549627
  2. Differences in active-site microarchitecture explain the dissimilar behaviors of PBP5 and 6 in Escherichia coli. Chowdhury C, et al. J Mol Graph Model, 2011 Feb. PMID 21163680
  3. Septal and lateral wall localization of PBP5, the major D,D-carboxypeptidase of Escherichia coli, requires substrate recognition and membrane attachment. Potluri L, et al. Mol Microbiol, 2010 Jul. PMID 20545860, Free PMC Article
  4. Deletion of penicillin-binding protein 5 (PBP5) sensitises Escherichia coli cells to beta-lactam agents. Sarkar SK, et al. Int J Antimicrob Agents, 2010 Mar. PMID 20047819
  5. Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle. Sauvage E, et al. J Mol Biol, 2008 Aug 29. PMID 18602645, Free PMC Article

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.
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General gene information

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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 hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
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
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 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 membrane IEA
Inferred from Electronic Annotation
more info
  
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
    A0A827XV09
    Conserved Domains (1) summary
    PRK10793
    Location:1 → 403
    PRK10793; D-alanyl-D-alanine carboxypeptidase fraction A; Provisional
Nucleotide Protein
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