RegulonDB RegulonDB 11.0: Gene Form
   

ldtA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cobT ldtA asnV terminator erfKp4 erfKp4 TSS_2303 TSS_2303 TSS_2302 (cluster) TSS_2302 (cluster) TSS_2301 TSS_2301 TSS_2300 TSS_2300

Gene      
Name: ldtA    Texpresso search in the literature
Synonym(s): ECK1985, G7073, b1990, erfK, yeeG, yzzT
Genome position(nucleotides): 2062391 <-- 2063323
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.62
External database links:  
ASAP:
 ABE-0006607
ECHOBASE:
 EB2546
ECOLIHUB:
 erfK
OU-MICROARRAY:
 b1990
STRING:
 511145.b1990
COLOMBOS: ldtA


Product      
Name: L,D-transpeptidase LdtA
Synonym(s): ErfK, LdtA, YeeG, YzzT
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 34.411
Isoelectric point: 8.931
Motif(s):
 
Type Positions Sequence Comment
1 -> 21 MRRVNILCSFALLFASHTSLA
22 -> 310 VTYPLPPEGSRLVGQSFTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQLILPDTVRKGIVVNVAEMRLYYYPPDSNTVEVFPIGIGQAGRETPRNWVTTVERKQEAPTWTPTPNTRREYAKRGESLPAFVPAGPDNPMGLYAIYIGRLYAIHGTNANFGIGLRVSQGCIRLRNDDIKYLFDNVPVGTRVQIIDQPVKYTTEPDGSNWLEVHEPLSRNRAEYESDRKVPLPVTPSLRAFINGQEVDVNRANAALQRRSGMPVQISSGSRQMF UniProt: Probable L,D-transpeptidase ErfK/SrfK.
28 -> 29 PE UniProt: In Ref. 5; AA sequence..
96 -> 230 KGIVVNVAEMRLYYYPPDSNTVEVFPIGIGQAGRETPRNWVTTVERKQEAPTWTPTPNTRREYAKRGESLPAFVPAGPDNPMGLYAIYIGRLYAIHGTNANFGIGLRVSQGCIRLRNDDIKYLFDNVPVGTRVQI
191 -> 209 HGTNANFGIGLRVSQGCIR

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0005515 - protein binding
GO:0016757 - glycosyltransferase activity
GO:0016787 - hydrolase activity
GO:0016740 - transferase activity
GO:0004180 - carboxypeptidase activity
GO:0071972 - peptidoglycan L,D-transpeptidase activity
biological_process GO:0006508 - proteolysis
GO:0009252 - peptidoglycan biosynthetic process
GO:0008360 - regulation of cell shape
GO:0018104 - peptidoglycan-protein cross-linking
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Reference(s): [1] Kuru E., et al., 2019
External database links:  
ALPHAFOLD:
 P39176
DIP:
 DIP-9522N
ECOCYC:
 G7073-MONOMER
ECOLIWIKI:
 b1990
INTERPRO:
 IPR038063
INTERPRO:
 IPR005490
INTERPRO:
 IPR041597
PFAM:
 PF17969
PFAM:
 PF03734
PRIDE:
 P39176
PRODB:
 PRO_000022531
REFSEQ:
 NP_416494
SMR:
 P39176
UNIPROT:
 P39176


Operon      
Name: ldtA         
Operon arrangement:
Transcription unit        Promoter
ldtA


RNA cis-regulatory element    
Attenuation: Translational


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_2300 2062260 forward nd [RS-EPT-CBR] [2]
  promoter TSS_2301 2062756 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2302 (cluster) 2062780 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_2303 2063353 reverse nd [RS-EPT-CBR] [2]
  promoter erfKp4 2063354 reverse nd [ICWHO] [3]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Kuru E., Radkov A., Meng X., Egan A., Alvarez L., Dowson A., Booher G., Breukink E., Roper DI., Cava F., Vollmer W., Brun Y., VanNieuwenhze MS., 2019, Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis., ACS Chem Biol 14(12):2745-2756

 [2] 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.

 [3] 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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