RegulonDB RegulonDB 10.9: Gene Form
   

ampD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

aroP nadC ampE ampD CRP TSS_235 TSS_235 TSS_234 (cluster) TSS_234 (cluster) TSS_233 TSS_233 ampD ampD ampDp5 ampDp5 nadCp nadCp TSS_232 TSS_232

Gene      
Name: ampD    Texpresso search in the literature
Synonym(s): ECK0109, EG10041, b0110
Genome position(nucleotides): 118733 --> 119284 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.8
External database links:  
ASAP:
ABE-0000380
CGSC:
30478
ECHOBASE:
EB0039
ECOLIHUB:
ampD
OU-MICROARRAY:
b0110
STRING:
511145.b0110
COLOMBOS: ampD


Product      
Name: 1,6-anhydro-N-acetylmuramoyl-L-alanine amidase
Synonym(s): AmpD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 20.536
Isoelectric point: 5.232
Motif(s):
 
Type Positions Sequence
30 -> 167 LLVVHNISLPPGEFGGPWIDALFTGTIDPQAHPFFAEIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSQYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTRALIDCYPDIAKNMTGHCDIAPDRKTDPGP
31 -> 167 LVVHNISLPPGEFGGPWIDALFTGTIDPQAHPFFAEIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSQYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTRALIDCYPDIAKNMTGHCDIAPDRKTDPGP

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.34 - murein turnover, recycling
  6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity
GO:0009392 - N-acetyl-anhydromuramoyl-L-alanine amidase activity
biological_process GO:0009254 - peptidoglycan turnover
GO:0009253 - peptidoglycan catabolic process
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Reference(s): [1] Jacobs C. 1997
[2] Petrosino JF., et al., 2009
[3] Tuomanen E., et al., 1991
External database links:  
ECOCYC:
EG10041-MONOMER
ECOLIWIKI:
b0110
INTERPRO:
IPR002502
INTERPRO:
IPR036505
MODBASE:
P13016
PFAM:
PF01510
PRIDE:
P13016
PRODB:
PRO_000022096
REFSEQ:
NP_414652
SMART:
SM00644
SMR:
P13016
SWISSMODEL:
P13016
UNIPROT:
P13016


Operon      
Name: ampDE         
Operon arrangement:
Transcription unit        Promoter
ampDE


Transcriptional Regulation      
Display Regulation             
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_232 118078 reverse nd [RS-EPT-CBR] [4]
  promoter ampDp5 118681 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter TSS_233 120916 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_234 (cluster) 120919 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [4]
  promoter TSS_235 120955 reverse nd [RS-EPT-CBR] [4]


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] Jacobs C., 1997, Pharmacia Biotech & Science prize. 1997 grand prize winner. Life in the balance: cell walls and antibiotic resistance., Science 278(5344):1731-2

 [2] Petrosino JF., Galhardo RS., Morales LD., Rosenberg SM., 2009, Stress-induced beta-lactam antibiotic resistance mutation and sequences of stationary-phase mutations in the Escherichia coli chromosome., J Bacteriol 191(19):5881-9

 [3] Tuomanen E., Lindquist S., Sande S., Galleni M., Light K., Gage D., Normark S., 1991, Coordinate regulation of beta-lactamase induction and peptidoglycan composition by the amp operon., Science 251(4990):201-4

 [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.

 [5] 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


RegulonDB