RegulonDB RegulonDB 10.9: Gene Form
   

ldtB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybiT ybiR ldtB mntR CRP AscG ybiTp ybiTp ldtBp ldtBp TSS_980 TSS_980

Gene      
Name: ldtB    Texpresso search in the literature
Synonym(s): ECK0809, G6422, b0819, ybiS
Genome position(nucleotides): 854824 <-- 855744 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.99
External database links:  
ASAP:
ABE-0002797
ECHOBASE:
EB3108
ECOLIHUB:
ybiS
OU-MICROARRAY:
b0819
STRING:
511145.b0819
COLOMBOS: ldtB


Product      
Name: L,D-transpeptidase LdtB
Synonym(s): LdtB, YbiS
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 33.325
Isoelectric point: 6.364
Motif(s):
 
Type Positions Sequence
101 -> 231 IVINSAEMRLYYYPKGTNTVIVLPIGIGQLGKDTPINWTTKVERKKAGPTWTPTAKMHAEYRAAGEPLPAVVPAGPDNPMGLYALYIGRLYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGTRV
210 -> 210 C
1 -> 24 MNMKLKTLFAAAFAVVGFCSTASA
25 -> 306 VTYPLPTDGSRLVGQNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQLILPDTVHEGIVINSAEMRLYYYPKGTNTVIVLPIGIGQLGKDTPINWTTKVERKKAGPTWTPTAKMHAEYRAAGEPLPAVVPAGPDNPMGLYALYIGRLYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGTRVQFIDEPVKATTEPDGSRYIEVHNPLSTTEAQFEGQEIVPITLTKSVQTVTGQPDVDQVVLDEAIKNRSGMPVRLN
194 -> 212 HGTNANFGIGLRVSHGCVR

 

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 - transferase activity, transferring glycosyl groups
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
[2] Zhai Y., et al., 2002
External database links:  
DIP:
DIP-48069N
ECOCYC:
G6422-MONOMER
ECOLIWIKI:
b0819
INTERPRO:
IPR005490
INTERPRO:
IPR038063
INTERPRO:
IPR041597
PFAM:
PF17969
PFAM:
PF03734
PRIDE:
P0AAX8
REFSEQ:
NP_415340
SMR:
P0AAX8
UNIPROT:
P0AAX8


Operon      
Name: ldtB         
Operon arrangement:
Transcription unit        Promoter
ldtB


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, Rob
Repressed by: CRP


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_980 855304 reverse 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] 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] Zhai Y., Saier MH., 2002, The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes., Protein Sci 11(9):2196-207

 [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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