RegulonDB RegulonDB 11.1: Gene Form
   

ldcA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cvrA ldcA emtA ymgM TSS_1520 TSS_1520 ldcAp9 ldcAp9 TSS_1519 TSS_1519 emtAp4 emtAp4 TSS_1518 (cluster) TSS_1518 (cluster) cvrAp6 cvrAp6 TSS_1517 TSS_1517

Gene      
Name: ldcA    Texpresso search in the literature
Synonym(s): ECK1180, G6621, b1192, ycgQ
Genome position(nucleotides): 1242166 <-- 1243080
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.01
External database links:  
ASAP:
 ABE-0004002
ECHOBASE:
 EB3657
ECOLIHUB:
 ldcA
ECOO157CYC:
 Z1955
OU-MICROARRAY:
 b1192
STRING:
 511145.b1192
COLOMBOS: ldcA


Product      
Name: murein tetrapeptide carboxypeptidase
Synonym(s): L,D-carboxypeptidase A, LdcA, YcgQ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 33.567
Isoelectric point: 6.576
Motif(s):
 
Type Positions Sequence Comment
5 -> 126 HLIAPSGYCIKQHAALRGIQRLTDAGHQVNNVEVIARRCERFAGTETERLEDLNSLARLTTPNTIVLAVRGGYGASRLLADIDWQALVARQQHDPLLICGHSDFTAIQCGLLAHGNVITFSG
169 -> 283 EGTLWGGNLAMLISLIGTPWMPKIENGILVLEDINEHPFRVERMLLQLYHAGILPRQKAIILGSFSGSTPNDYDAGYNLESVYAFLRSRLSIPLITGLDFGHEQRTVTLPLGAHA

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.3 - proteins/peptides/glycopeptides
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.34 - murein turnover, recycling
  6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0106415 - muramoyltetrapeptide carboxypeptidase activity
GO:0061787 - peptidoglycan cross-bridge peptide endopeptidase activity
GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0004180 - carboxypeptidase activity
GO:0008236 - serine-type peptidase activity
GO:0042803 - protein homodimerization activity
biological_process GO:0006508 - proteolysis
GO:0009252 - peptidoglycan biosynthetic process
GO:0009254 - peptidoglycan turnover
GO:0008360 - regulation of cell shape
GO:0071555 - cell wall organization
External database links:  
ALPHAFOLD:
 P76008
DIP:
 DIP-10085N
ECOCYC:
 G6621-MONOMER
ECOLIWIKI:
 b1192
ECOO157CYC:
 Z1955-MONOMER
INTERPRO:
 IPR027478
INTERPRO:
 IPR040449
INTERPRO:
 IPR040921
INTERPRO:
 IPR027461
INTERPRO:
 IPR003507
INTERPRO:
 IPR029062
PANTHER:
 PTHR30237
PDB:
 5Z01
PDB:
 5Z03
PFAM:
 PF17676
PFAM:
 PF02016
PRIDE:
 P76008
PRODB:
 PRO_000023074
REFSEQ:
 NP_415710
SMR:
 P76008
UNIPROT:
 P76008


Operon      
Name: ldcA         
Operon arrangement:
Transcription unit        Promoter
ldcA


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1517 1242102 reverse nd [RS-EPT-CBR] [1]
  promoter cvrAp6 1242164 reverse nd [COMP-AINF] [2]
  promoter TSS_1518 (cluster) 1243112 reverse nd [RS-EPT-CBR] [1]
  promoter emtAp4 1243125 forward nd [COMP-AINF] [2]
  promoter TSS_1519 1243161 reverse nd [RS-EPT-CBR] [1]
  promoter ldcAp9 1243197 reverse nd [COMP-AINF] [2]
  promoter TSS_1520 1243371 forward nd [RS-EPT-CBR] [1]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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