RegulonDB RegulonDB 11.1: Gene Form
   

nlpD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nlpD rpoS pcm umpG MqsA ArcA CRP ArcA CRP DksA-ppGpp DksA-ppGpp ppGpp terminator nlpDp1 nlpDp1 nlpDp2 nlpDp2 TSS_3034 TSS_3034 rpoSp rpoSp rpoSp4 rpoSp4 rpoSp3 rpoSp3 TSS_3032 TSS_3032 rpoSp2 rpoSp2 TSS_3031 TSS_3031 rpoSp1 rpoSp1 TSS_3030 TSS_3030 TSS_3029 TSS_3029 TSS_3028 TSS_3028 TSS_3027 TSS_3027 TSS_3026 TSS_3026

Gene      
Name: nlpD    Texpresso search in the literature
Synonym(s): ECK2737, EG12111, b2742
Genome position(nucleotides): 2867614 <-- 2868753
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.46
External database links:  
ASAP:
 ABE-0009004
CGSC:
 33225
ECHOBASE:
 EB2034
ECOLIHUB:
 nlpD
OU-MICROARRAY:
 b2742
STRING:
 511145.b2742
COLOMBOS: nlpD


Shine dalgarno      
Sequence: caatttttccTGGGGGataAAT


Product      
Name: murein hydrolase activator NlpD
Synonym(s): NlpD, NlpD divisome associated factor, activates peptidoglycan hydrolase
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,outer membrane
Molecular weight: 40.149
Isoelectric point: 9.926
Motif(s):
 
Type Positions Sequence Comment
1 -> 25 MSAGSPKFTVRRIAALSLVSLWLAG
26 -> 379 CSDTSNPPAPVSSVNGNAPANTNSGMLITPPPKMGTTSTAQQPQIQPVQQPQIQATQQPQIQPVQPVAQQPVQMENGRIVYNRQYGNIPKGSYSGSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYALNVGQTLQVGNASGTPITGGNAITQADAAEQGVVIKPAQNSTVAVASQPTITYSESSGEQSANKMLPNNKPTATTVTAPVTVPTASTTEPTVSSTSTSTPISTWRWPTEGKVIETFGASEGGNKGIDIAGSKGQAIIATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTSSTRLHFEIRYKGKSVNPLRYLPQR UniProt: Murein hydrolase activator NlpD.
29 -> 64 TSNPPAPVSSVNGNAPANTNSGMLITPPPKMGTTST N-terminal disordered linker that is implicated in OM targeting
30 -> 67 SNPPAPVSSVNGNAPANTNSGMLITPPPKMGTTSTAQQ UniProt: Disordered; Sequence Annotation Type: region of interest.
66 -> 97 QQPQIQPVQQPQIQATQQPQIQPVQPVAQQPV UniProt: 4 X 8 AA tandem repeats of Q-Q-P-Q-I-Q-P-V; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.1 - cell division
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0032153 - cell division site
molecular_function GO:0004222 - metalloendopeptidase activity
biological_process GO:0051301 - cell division
GO:0006508 - proteolysis
GO:0007049 - cell cycle
GO:0009410 - response to xenobiotic stimulus
GO:0051345 - positive regulation of hydrolase activity
GO:0000920 - septum digestion after cytokinesis
Note(s): Note(s): ...[more].
Reference(s): [1] Rao S., et al., 2020
[2] Yang DC., et al., 2012
External database links:  
ALPHAFOLD:
 P0ADA3
DIP:
 DIP-48067N
ECOCYC:
 EG12111-MONOMER
ECOLIWIKI:
 b2742
INTERPRO:
 IPR018392
INTERPRO:
 IPR036779
INTERPRO:
 IPR016047
INTERPRO:
 IPR011055
MODBASE:
 P0ADA3
PFAM:
 PF01551
PFAM:
 PF01476
PRIDE:
 P0ADA3
PRODB:
 PRO_000023394
PROSITE:
 PS51257
PROSITE:
 PS51782
REFSEQ:
 NP_417222
SMART:
 SM00257
SMR:
 P0ADA3
UNIPROT:
 P0ADA3


Operon      
Name: nlpD-rpoS         
Operon arrangement:
Transcription unit        Promoter
rpoS
rpoS
rpoS
rpoS
rpoS
nlpD-rpoS
nlpD-rpoS


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_3026 2866797 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3027 2867113 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3028 2867456 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3029 2867493 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3030 2867551 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3031 2867572 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3032 2867645 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3034 2868128 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] Rao S., Bates GT., Matthews CR., Newport TD., Vickery ON., Stansfeld PJ., 2020, Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations., Structure 28(4):475-487.e3

 [2] Yang DC., Tan K., Joachimiak A., Bernhardt TG., 2012, A conformational switch controls cell wall-remodelling enzymes required for bacterial cell division., Mol Microbiol 85(4):768-81

 [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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