RegulonDB RegulonDB 11.2: Gene Form
   

ldtD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mukB ldtD mepK CpxR TSS_1205 TSS_1205 TSS_1204 TSS_1204 TSS_1203 (cluster) TSS_1203 (cluster) TSS_1202 TSS_1202 TSS_1201 TSS_1201 TSS_1200 TSS_1200 mepKp mepKp TSS_1198 TSS_1198 ldtDp ldtDp TSS_1197 TSS_1197 TSS_1196 TSS_1196 TSS_1195 TSS_1195

Gene      
Name: ldtD    Texpresso search in the literature
Synonym(s): ECK0916, EG11253, b0925, ycbB
Genome position(nucleotides): 981047 --> 982894
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.14
External database links:  
ASAP:
 ABE-0003142
ECHOBASE:
 EB1233
ECOLIHUB:
 ycbB
OU-MICROARRAY:
 b0925
STRING:
 511145.b0925
COLOMBOS: ldtD


Product      
Name: L,D-transpeptidase LdtD
Synonym(s): LdtD, YcbB
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space,inner membrane
Molecular weight: 67.812
Isoelectric point: 8.712
Motif(s):
 
Type Positions Sequence Comment
11 -> 26 LSAISLCLAVTFAPLF UniProt: Helical.
39 -> 40 DS UniProt: In Ref. 4; CAA40777..
93 -> 224 QLQLLYAARDMQPMWENRDAVKAFQQQLAEVAIAGFQPQFNKWVELLTDPGVNGMARDVVLSDAMMGYLHFIANIPVKGTRWLYSSKPYALATPPLSVINQWQLALDKGQLPTFVAGLAPQHPQYAAMHESL
268 -> 312 GPKITLPGDDTPTDAVVSPSAVTVETAETKPMDKQTTSRSKPAPA Δ268-312: loss of non-carbapenem β-lactam resistance (ampicillin, ceftriaxone) in vivo
288 -> 309 AVTVETAETKPMDKQTTSRSKP UniProt: Polar residues; Sequence Annotation Type: compositionally biased region.

 
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:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0005515 - protein binding
GO:0016757 - glycosyltransferase activity
GO:0016787 - hydrolase activity
GO:0016740 - transferase activity
GO:0004180 - carboxypeptidase activity
GO:0016807 - cysteine-type carboxypeptidase activity
GO:0071972 - peptidoglycan L,D-transpeptidase activity
biological_process GO:0006508 - proteolysis
GO:0006974 - cellular response to DNA damage stimulus
GO:0009252 - peptidoglycan biosynthetic process
GO:0046677 - response to antibiotic
GO:0008360 - regulation of cell shape
GO:0018104 - peptidoglycan-protein cross-linking
GO:0071555 - cell wall organization
GO:0036460 - cellular response to cell envelope stress
Note(s): Note(s): ...[more].
Reference(s): [1] Hugonnet JE., et al., 2016
[2] Kuru E., et al., 2019
External database links:  
ALPHAFOLD:
 P22525
DIP:
 DIP-11474N
ECOCYC:
 EG11253-MONOMER
ECOLIWIKI:
 b0925
INTERPRO:
 IPR038063
INTERPRO:
 IPR036365
INTERPRO:
 IPR002477
INTERPRO:
 IPR005490
MODBASE:
 P22525
PDB:
 6NTW
PFAM:
 PF01471
PFAM:
 PF03734
PFAM:
 PF20142
PRIDE:
 P22525
PROSITE:
 PS00092
REFSEQ:
 NP_415445
SMR:
 P22525
UNIPROT:
 P22525


Operon      
Name: ldtD         
Operon arrangement:
Transcription unit        Promoter
ldtD


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_1195 979917 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1196 980088 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1197 980108 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1198 983021 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1200 983050 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1201 983052 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1202 983510 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1203 (cluster) 983574 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1204 983579 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1205 983585 forward nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Hugonnet JE., Mengin-Lecreulx D., Monton A., den Blaauwen T., Carbonnelle E., Veckerle C., Brun YV., van Nieuwenhze M., Bouchier C., Tu K., Rice LB., Arthur M., 2016, Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli., Elife 5

 [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] 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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