RegulonDB RegulonDB 11.2: Gene Form
   

ldtC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mfd ldtC bhsB bhsA CpxR TSS_1444 (cluster) TSS_1444 (cluster) TSS_1443 TSS_1443 ldtCp ldtCp

Gene      
Name: ldtC    Texpresso search in the literature
Synonym(s): ECK1099, G6571, b1113, ycfS
Genome position(nucleotides): 1169412 <-- 1170374
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.27
External database links:  
ASAP:
 ABE-0003760
ECHOBASE:
 EB3211
ECOLIHUB:
 ycfS
OU-MICROARRAY:
 b1113
STRING:
 511145.b1113
COLOMBOS: ldtC


Product      
Name: L,D-transpeptidase LdtC
Synonym(s): LdtC, YcfS
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 34.636
Isoelectric point: 9.209
Motif(s):
 
Type Positions Sequence Comment
1 -> 23 MMIKTRFSRWLTFFTFAAAVALA
24 -> 320 LPAKANTWPLPPAGSRLVGENKFHVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTIPLQTLLPDAPREGIVINIAELRLYYYPPGKNSVTVYPIGIGQLGGDTLTPTMVTTVSDKRANPTWTPTANIRARYKAQGIELPAVVPAGLDNPMGHHAIRLAAYGGVYLLHGTNADFGIGMRVSSGCIRLRDDDIKTLFSQVTPGTKVNIINTPIKVSAEPNGARLVEVHQPLSEKIDDDPQLLPITLNSAMQSFKDAAQTDAEVMQHVMDVRSGMPVDVRRHQVSPQTL UniProt: Probable L,D-transpeptidase YcfS.
45 -> 90 KFHVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTI UniProt: LysM.
47 -> 91 HVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTIP
103 -> 240 GIVINIAELRLYYYPPGKNSVTVYPIGIGQLGGDTLTPTMVTTVSDKRANPTWTPTANIRARYKAQGIELPAVVPAGLDNPMGHHAIRLAAYGGVYLLHGTNADFGIGMRVSSGCIRLRDDDIKTLFSQVTPGTKVNI

 
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] Egler M., et al., 2005
[2] Kuru E., et al., 2019
[3] Machas M., et al., 2021
External database links:  
ALPHAFOLD:
 P75954
DIP:
 DIP-11546N
ECOCYC:
 G6571-MONOMER
ECOLIWIKI:
 b1113
INTERPRO:
 IPR041597
INTERPRO:
 IPR038063
INTERPRO:
 IPR018392
INTERPRO:
 IPR005490
PFAM:
 PF03734
PFAM:
 PF17969
PFAM:
 PF01476
PRIDE:
 P75954
PROSITE:
 PS51782
REFSEQ:
 NP_415631
SMART:
 SM00257
SMR:
 P75954
UNIPROT:
 P75954


Operon      
Name: ldtC         
Operon arrangement:
Transcription unit        Promoter
ldtC


Transcriptional Regulation      
Display Regulation             
Activated by: CpxR


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_1443 1171800 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_1444 (cluster) 1173832 reverse nd [RS-EPT-CBR] [4]


Evidence    

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


Reference(s)    

 [1] Egler M., Grosse C., Grass G., Nies DH., 2005, Role of the extracytoplasmic function protein family sigma factor RpoE in metal resistance of Escherichia coli., J Bacteriol 187(7):2297-307

 [2] 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

 [3] Machas M., Kurgan G., Abed OA., Shapiro A., Wang X., Nielsen D., 2021, Characterizing Escherichia coli's transcriptional response to different styrene exposure modes reveals novel toxicity and tolerance insights., J Ind Microbiol Biotechnol 48(1-2)

 [4] 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.

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