RegulonDB RegulonDB 11.1: Gene Form
   

nirD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

Gene      
Name: nirD    Texpresso search in the literature
Synonym(s): ECK3354, EG10655, b3366
Genome position(nucleotides): 3496551 --> 3496877
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.96
External database links:  
ASAP:
 ABE-0011005
CGSC:
 35425
ECHOBASE:
 EB0649
ECOLIHUB:
 nirD
OU-MICROARRAY:
 b3366
STRING:
 511145.b3366
COLOMBOS: nirD


Product      
Name: nitrite reductase (NADH) small subunit
Synonym(s): NirD, nitrite reductase subunit NirD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 12.284
Isoelectric point: 4.876
Motif(s):
 
Type Positions Sequence Comment
3 -> 106 QWKDICKIDDILPETGVCALLGDEQVAIFRPYHSDQVFAISNIDPFFESSVLSRGLIAEHQGELWVASPLKKQRFRLSDGLCMEDEQFSVKHYEARVKDGVVQL
102 -> 102 G UniProt: In Ref. 1 and 2..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.8 - metabolism of other compounds --> 1.8.3 - nitrogen metabolism
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0009344 - nitrite reductase complex [NAD(P)H]
molecular_function GO:0106316 - nitrite reductase NADH activity
GO:0005515 - protein binding
GO:0016491 - oxidoreductase activity
GO:0051537 - 2 iron, 2 sulfur cluster binding
GO:0008942 - nitrite reductase [NAD(P)H] activity
biological_process GO:0051348 - negative regulation of transferase activity
GO:0009061 - anaerobic respiration
GO:0042128 - nitrate assimilation
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA] Inferred from direct assay
Reference(s): [1] Abou-Jaoude A., et al., 1978
[2] Leger L., et al., 2021
[3] MacDonald H., et al., 1985
[4] Peakman T., et al., 1990
External database links:  
ALPHAFOLD:
 P0A9I8
ECOCYC:
 NIRD-MONOMER
ECOLIWIKI:
 b3366
INTERPRO:
 IPR036922
INTERPRO:
 IPR017881
INTERPRO:
 IPR012748
MODBASE:
 P0A9I8
PANTHER:
 PTHR40562
PDB:
 2JO6
PFAM:
 PF13806
PRIDE:
 P0A9I8
PRODB:
 PRO_000023391
PROSITE:
 PS51300
REFSEQ:
 NP_417825
SMR:
 P0A9I8
UNIPROT:
 P0A9I8


Operon      
Name: nirBDC-cysG         
Operon arrangement:
Transcription unit        Promoter
nirBDC-cysG
cysG
cysG


Transcriptional Regulation      
Display Regulation             
Activated by: FNR, IHF, NarL, NarP
Repressed by: CRP, H-NS, IHF, Cra, Fis


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_3967 3493998 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3968 (cluster) 3494032 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3969 3494035 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3970 3494404 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3971 3494422 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3972 3494535 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3973 3494981 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3974 3495073 forward nd [RS-EPT-CBR] [5]
  promoter TSS_3975 3495419 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_3976 3496522 forward nd [RS-EPT-CBR] [5]


Evidence    

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


Reference(s)    

 [1] Abou-Jaoude A., Lepelletier M., Ratouchniak J., Chippaux M., Pascal MC., 1978, Nitrite reduction in Escherichia coli: genetic analysis of nir mutants., Mol Gen Genet 167(1):113-8

 [2] Leger L., Byrne D., Guiraud P., Germain E., Maisonneuve E., 2021, NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli., Elife 10

 [3] MacDonald H., Pope NR., Cole JA., 1985, Isolation, characterization and complementation analysis of nirB mutants of Escherichia coli deficient only in NADH-dependent nitrite reductase activity., J Gen Microbiol 131(10):2771-82

 [4] Peakman T., Crouzet J., Mayaux JF., Busby S., Mohan S., Harborne N., Wootton J., Nicolson R., Cole J., 1990, Nucleotide sequence, organisation and structural analysis of the products of genes in the nirB-cysG region of the Escherichia coli K-12 chromosome., Eur J Biochem 191(2):315-23

 [5] 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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