RegulonDB RegulonDB 11.1: Gene Form
   

nirB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nirB tsgA nirC nirD Fis Cra FNR CRP NarL NarP NarL NarP IHF Fis IHF Fis CRP RyhB terminator anti-terminator anti-anti-terminator cysGp2 cysGp2 cysGp1 cysGp1 TSS_3976 TSS_3976 TSS_3975 TSS_3975 TSS_3974 TSS_3974 TSS_3973 TSS_3973 TSS_3972 TSS_3972 TSS_3971 TSS_3971 TSS_3970 TSS_3970 TSS_3969 TSS_3969 TSS_3968 (cluster) TSS_3968 (cluster) TSS_3967 TSS_3967 nirBp nirBp

Gene      
Name: nirB    Texpresso search in the literature
Synonym(s): ECK3353, EG10653, b3365
Genome position(nucleotides): 3494011 --> 3496554
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.28
External database links:  
ASAP:
 ABE-0011003
CGSC:
 451
ECHOBASE:
 EB0647
ECOLIHUB:
 nirB
OU-MICROARRAY:
 b3365
STRING:
 511145.b3365
COLOMBOS: nirB


Product      
Name: nitrite reductase (NADH) large subunit
Synonym(s): NirB, nitrite reductase catalytic subunit NirB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 93.121
Isoelectric point: 6.071
Motif(s):
 
Type Positions Sequence Comment
5 -> 292 RLAIIGNGMVGHRFIEDLLDKSDAANFDITVFCEEPRIAYDRVHLSSYFSHHTAEELSLVREGFYEKHGIKVLVGERAITINRQEKVIHSSAGRTVFYDKLIMATGSYPWIPPIKGSDTQDCFVYRTIEDLNAIESCARRSKRGAVVGGGLLGLEAAGALKNLGIETHVIEFAPMLMAEQLDQMGGEQLRRKIESMGVRVHTSKNTLEIVQEGVEARKTMRFADGSELEVDFIVFSTGIRPRDKLATQCGLDVAPRGGIVINDSCQTSDPDIYAIGECASWNNRVFGL
44 -> 79 YDRVHLSSYFSHHTAEELSLVREGFYEKHGIKVLVG UniProt: FAD.
193 -> 225 LRRKIESMGVRVHTSKNTLEIVQEGVEARKTMR UniProt: NAD or NADP.
321 -> 387 AKLKLLGVDVGGIGDAHGRTPGARSYVYLDESKEIYKRLIVSEDNKTLLGAVLVGDTSDYGNLLQLV
424 -> 471 ICSCFDVTKGDLIAAINKGCHTVAALKAETKAGTGCGGCIPLVTQVLN

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.8 - metabolism of other compounds --> 1.8.3 - nitrogen metabolism
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0009344 - nitrite reductase complex [NAD(P)H]
molecular_function GO:0106316 - nitrite reductase NADH activity
GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0050660 - flavin adenine dinucleotide binding
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0051537 - 2 iron, 2 sulfur cluster binding
GO:0008942 - nitrite reductase [NAD(P)H] activity
GO:0020037 - heme binding
GO:0050661 - NADP binding
biological_process GO:0006116 - NADH oxidation
GO:0006113 - fermentation
GO:0042128 - nitrate assimilation
Note(s): Note(s): ...[more].
Reference(s): [1] Chong H., et al., 2014
[2] Cole JA., et al., 1980
[3] Page L., et al., 1990
[4] Peakman T., et al., 1990
External database links:  
ALPHAFOLD:
 P08201
ECOCYC:
 NIRB-MONOMER
ECOLIWIKI:
 b3365
INTERPRO:
 IPR007419
INTERPRO:
 IPR012744
INTERPRO:
 IPR017121
INTERPRO:
 IPR023753
INTERPRO:
 IPR036136
INTERPRO:
 IPR036188
INTERPRO:
 IPR006067
INTERPRO:
 IPR006066
INTERPRO:
 IPR005117
INTERPRO:
 IPR041575
INTERPRO:
 IPR041854
MODBASE:
 P08201
PFAM:
 PF03460
PFAM:
 PF18267
PFAM:
 PF07992
PFAM:
 PF04324
PFAM:
 PF01077
PRIDE:
 P08201
PRINTS:
 PR00397
PROSITE:
 PS00365
REFSEQ:
 NP_417824
SMR:
 P08201
UNIPROT:
 P08201


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


Regulation by small RNA    
  Display Regulation
small RNA ryhB


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] Chong H., Geng H., Zhang H., Song H., Huang L., Jiang R., 2014, Enhancing E. coli isobutanol tolerance through engineering its global transcription factor cAMP receptor protein (CRP)., Biotechnol Bioeng 111(4):700-8

 [2] Cole JA., Newman BM., White P., 1980, Biochemical and genetic characterization of nirB mutants of Escherichia coli K 12 pleiotropically defective in nitrite and sulphite reduction., J Gen Microbiol 120(2):475-83

 [3] Page L., Griffiths L., Cole JA., 1990, Different physiological roles of two independent pathways for nitrite reduction to ammonia by enteric bacteria., Arch Microbiol 154(4):349-54

 [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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