RegulonDB RegulonDB 11.1: Gene Form
   

ldtE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ldtE sufE lpp MicL-S ynhGp4 ynhGp4 ynhGp7 ynhGp7 TSS_1985 TSS_1985 TSS_1984 TSS_1984 TSS_1983 TSS_1983 TSS_1982 (cluster) TSS_1982 (cluster) TSS_1981 TSS_1981

Gene      
Name: ldtE    Texpresso search in the literature
Synonym(s): ECK1674, G6904, b1678, ynhG
Genome position(nucleotides): 1757721 <-- 1758725
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.84
External database links:  
ASAP:
 ABE-0005605
ECHOBASE:
 EB3771
ECOLIHUB:
 ynhG
OU-MICROARRAY:
 b1678
STRING:
 511145.b1678
COLOMBOS: ldtE


Product      
Name: L,D-transpeptidase LdtE
Synonym(s): LdtE, YnhG
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 36.082
Isoelectric point: 9.765
Motif(s):
 
Type Positions Sequence Comment
1 -> 23 MKRASLLTLTLIGAFSAIQAAWA
24 -> 334 VDYPLPPTGSRLVGQNQTYTVQEGDKNLQAIARRFDTAAMLILEANNTIAPVPKPGTTITIPSQLLLPDAPRQGIIVNLAELRLYYYPPGENIVQVYPIGIGLQGLETPVMETRVGQKIPNPTWTPTAGIRQRSLERGIKLPPVVPAGPNNPLGRYALRLAHGNGEYLIHGTSAPDSVGLRVSSGCIRMNAPDIKALFSSVRTGTPVKVINEPVKYSVEPNGMRYVEVHRPLSAEEQQNVQTMPYTLPAGFTQFKDNKAVDQKLVDKALYRRAGYPVSVSSGATPAASNAPSVESAQNGEPEQGNMLRVTQ UniProt: Probable L,D-transpeptidase YnhG.
40 -> 84 QTYTVQEGDKNLQAIARRFDTAAMLILEANNTIAPVPKPGTTITI UniProt: LysM.
42 -> 85 YTVQEGDKNLQAIARRFDTAAMLILEANNTIAPVPKPGTTITIP
97 -> 232 GIIVNLAELRLYYYPPGENIVQVYPIGIGLQGLETPVMETRVGQKIPNPTWTPTAGIRQRSLERGIKLPPVVPAGPNNPLGRYALRLAHGNGEYLIHGTSAPDSVGLRVSSGCIRMNAPDIKALFSSVRTGTPVKV

 
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: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:
 P76193
DIP:
 DIP-12774N
ECOCYC:
 G6904-MONOMER
ECOLIWIKI:
 b1678
INTERPRO:
 IPR038063
INTERPRO:
 IPR041597
INTERPRO:
 IPR018392
INTERPRO:
 IPR005490
MODBASE:
 P76193
PFAM:
 PF03734
PFAM:
 PF01476
PFAM:
 PF17969
PRIDE:
 P76193
PROSITE:
 PS51782
REFSEQ:
 NP_416193
SMART:
 SM00257
SMR:
 P76193
UNIPROT:
 P76193


Operon      
Name: ldtE         
Operon arrangement:
Transcription unit        Promoter
ldtE


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_1981 1757425 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1982 (cluster) 1757506 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1983 1757512 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1984 1758859 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1985 1758864 reverse nd [RS-EPT-CBR] [2]
  promoter ynhGp7 1758944 reverse nd [COMP-AINF] [3]
  promoter ynhGp4 1758945 reverse nd [COMP-AINF] [3]


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] 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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