RegulonDB RegulonDB 10.8: Gene Form
   

arnD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

arnA arnT arnC arnD arnE TSS_2518 TSS_2518 TSS_2517 TSS_2517

Gene      
Name: arnD    Texpresso search in the literature
Synonym(s): ECK2249, G7169, b2256, pmrJ, yfbH
Genome position(nucleotides): 2370018 --> 2370908 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.86
External database links:  
ASAP:
 ABE-0007462
ECHOBASE:
 EB3845
OU-MICROARRAY:
 b2256
PortEco:
 arnD
STRING:
 511145.b2256
COLOMBOS: arnD


Product      
Name: putative 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD
Synonym(s): ArnD, PmrJ, YfbH
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 33.112
Isoelectric point: 7.644
Motif(s):
 
Type Positions Sequence
2 -> 260 TKVGLRIDVDTFRGTREGVPRLLEILSKHNIQASIFFSVGPDNMGRHLWRLVKPQFLWKMLRSNAASLYGWDILLAGTAWPGKEIGHANADIIREAAKHHEVGLHAWDHHAWQARSGNWDRQTMIDDIARGLRTLEEIIGQPVTCSAAAGWRADQKVIEAKEAFHLRYNSDCRGAMPFRPLLESGNPGTAQIPVTLPTWDEVIGRDVKAEDFNGWLLNRILRDKGTPVYTIHAEVEGCAYQHNFVDLLKRAAQEGVTFC
15 -> 167 GTREGVPRLLEILSKHNIQASIFFSVGPDNMGRHLWRLVKPQFLWKMLRSNAASLYGWDILLAGTAWPGKEIGHANADIIREAAKHHEVGLHAWDHHAWQARSGNWDRQTMIDDIARGLRTLEEIIGQPVTCSAAAGWRADQKVIEAKEAFHL

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016787 - hydrolase activity
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016811 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
biological_process GO:0005975 - carbohydrate metabolic process
GO:0006629 - lipid metabolic process
GO:0009103 - lipopolysaccharide biosynthetic process
GO:0009245 - lipid A biosynthetic process
GO:0046677 - response to antibiotic
GO:0010041 - response to iron(III) ion
GO:0036108 - 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process
Note(s): Note(s): ...[more].
Evidence: [AH] Author hypothesis
Reference(s): [1] Breazeale SD., et al., 2005
[2] Gibbons HS., et al., 2005
[3] Groisman EA. 2001
[4] Nummila K., et al., 1995
[5] Trent MS., et al., 2001
[6] Zhou Z., et al., 1999
External database links:  
ECOCYC:
 G7169-MONOMER
ECOLIWIKI:
 b2256
INTERPRO:
 IPR002509
INTERPRO:
 IPR023557
INTERPRO:
 IPR011330
MODBASE:
 P76472
PFAM:
 PF01522
PRIDE:
 P76472
PROSITE:
 PS51677
REFSEQ:
 NP_416759
SMR:
 P76472
UNIPROT:
 P76472


Operon      
Name: arnBCADTEF         
Operon arrangement:
Transcription unit        Promoter
 


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_2517 2367228 forward nd [RS-EPT-CBR] [7]
  promoter TSS_2518 2369128 forward nd [RS-EPT-CBR] [7]


Evidence    

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


Reference(s)    

 [1] Breazeale SD., Ribeiro AA., McClerren AL., Raetz CR., 2005, A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-Amino-4-deoxy-L-arabinose. Identification and function oF UDP-4-deoxy-4-formamido-L-arabinose., J Biol Chem 280(14):14154-67

 [2] Gibbons HS., Kalb SR., Cotter RJ., Raetz CR., 2005, Role of Mg2+ and pH in the modification of Salmonella lipid A after endocytosis by macrophage tumour cells., Mol Microbiol 55(2):425-40

 [3] Groisman EA., 2001, The pleiotropic two-component regulatory system PhoP-PhoQ., J Bacteriol 183(6):1835-42

 [4] Nummila K., Kilpelainen I., Zahringer U., Vaara M., Helander IM., 1995, Lipopolysaccharides of polymyxin B-resistant mutants of Escherichia coli are extensively substituted by 2-aminoethyl pyrophosphate and contain aminoarabinose in lipid A., Mol Microbiol 16(2):271-8

 [5] Trent MS., Ribeiro AA., Doerrler WT., Lin S., Cotter RJ., Raetz CR., 2001, Accumulation of a polyisoprene-linked amino sugar in polymyxin-resistant Salmonella typhimurium and Escherichia coli: structural characterization and transfer to lipid A in the periplasm., J Biol Chem 276(46):43132-44

 [6] Zhou Z., Lin S., Cotter RJ., Raetz CR., 1999, Lipid A modifications characteristic of Salmonella typhimurium are induced by NH4VO3 in Escherichia coli K12. Detection of 4-amino-4-deoxy-L-arabinose, phosphoethanolamine and palmitate., J Biol Chem 274(26):18503-14

 [7] 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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