RegulonDB RegulonDB 10.6.3: 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 NarP NarL NarP NarL IHF Fis IHF Fis CRP 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 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.28
External database links:  
ASAP:
ABE-0011003
CGSC:
451
ECHOBASE:
EB0647
ECOCYC:
EG10653
ECOLIHUB:
nirB
OU-MICROARRAY:
b3365
REGULONDB:
b3365
STRING:
511145.b3365
M3D: nirB
COLOMBOS: nirB
PortEco: b3365


Product      
Name: nitrite reductase catalytic subunit NirB
Synonym(s): NirB, nitrite reductase large subunit
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 93.121
Isoelectric point: 6.071
Motif(s):
 
Type Positions Sequence
5 -> 292 RLAIIGNGMVGHRFIEDLLDKSDAANFDITVFCEEPRIAYDRVHLSSYFSHHTAEELSLVREGFYEKHGIKVLVGERAITINRQEKVIHSSAGRTVFYDKLIMATGSYPWIPPIKGSDTQDCFVYRTIEDLNAIESCARRSKRGAVVGGGLLGLEAAGALKNLGIETHVIEFAPMLMAEQLDQMGGEQLRRKIESMGVRVHTSKNTLEIVQEGVEARKTMRFADGSELEVDFIVFSTGIRPRDKLATQCGLDVAPRGGIVINDSCQTSDPDIYAIGECASWNNRVFGL
321 -> 388 AKLKLLGVDVGGIGDAHGRTPGARSYVYLDESKEIYKRLIVSEDNKTLLGAVLVGDTSDYGNLLQLVL
442 -> 442 G
633 -> 757 KALRMAKTCVGSTWCRYGVGDSVGLGVELENRYKGIRTPHKMKFGVSGCTRECSEAQGKDVGIIATEKGWNLYVCGNGGMKPRHADLLAADIDRETLIKYLDRFMMFYIRTADKLTRTAPWLENL
193 -> 225 LRRKIESMGVRVHTSKNTLEIVQEGVEARKTMR

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0009344 - nitrite reductase complex [NAD(P)H]
molecular_function 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:0008942 - nitrite reductase [NAD(P)H] activity
GO:0020037 - heme binding
GO:0050661 - NADP binding
biological_process GO:0009061 - anaerobic respiration
GO:0042128 - nitrate assimilation
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
NIRB-MONOMER
ECOLIWIKI:
b3365
INTERPRO:
IPR007419
INTERPRO:
IPR036188
INTERPRO:
IPR036136
INTERPRO:
IPR023753
INTERPRO:
IPR017121
INTERPRO:
IPR005117
INTERPRO:
IPR006066
INTERPRO:
IPR006067
INTERPRO:
IPR012744
MODBASE:
P08201
PFAM:
PF01077
PFAM:
PF03460
PFAM:
PF04324
PFAM:
PF07992
PRIDE:
P08201
PRINTS:
PR00397
PROSITE:
PS00365
PROTEINMODELPORTAL:
P08201
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
Growth Conditions:

[1] 

C: Escherichia coli| rich medium| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| rich medium| sodium nitrite 2.5 mM| 37.0 C| OD650 from 0.5 to 0.7

[2] 

C: Escherichia coli| poor medium| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| poor medium| sodium nitrate 20 mM| 37.0 C| OD650 from 0.5 to 0.7

[3] 

C: Escherichia coli| poor medium| sodium nitrate 20 mM| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| cra knockout mutant| poor medium| sodium nitrate 20 mM| 37.0 C| OD650 from 0.5 to 0.7

[4] 

C: Escherichia coli| poor medium| sodium nitrite 2.5 mM| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| cra knockout mutant| poor medium| sodium nitrite 2.5 mM| 37.0 C| OD650 from 0.5 to 0.7

[5] 

C: Escherichia coli| rich medium| sodium nitrate 20 mM| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| poor medium| sodium nitrate 20 mM| 37.0 C| OD650 from 0.5 to 0.7

[6] 

C: Escherichia coli| poor medium| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| poor medium| sodium nitrite 2.5 mM| 37.0 C| OD650 from 0.5 to 0.7

[7] 

C: Escherichia coli| poor medium| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| cra knockout mutant| poor medium| 37.0 C| OD650 from 0.5 to 0.7

[8] 

C: Escherichia coli| rich medium| 37.0 C| OD650 from 0.5 to 0.7
E: Escherichia coli| rich medium| sodium nitrate 20 mM| 37.0 C| OD650 from 0.5 to 0.7



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] [1]
  promoter TSS_3968 (cluster) 3494032 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_3969 3494035 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3970 3494404 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3971 3494422 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3972 3494535 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3973 3494981 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3974 3495073 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3975 3495419 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3976 3496522 forward nd [RS-EPT-CBR] [1]


Evidence    

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



Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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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