RegulonDB RegulonDB 10.9: Gene Form
   

nrfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

acs nrfA nrfB nrfC Fis NarL FNR NarL IHF NsrR NarP NarL NarP NarL IHF NsrR IHF CRP Fis CRP Fis terminator TSS_4902 TSS_4902 nrfAp nrfAp acsp1 acsp1 acsp2 acsp2

Gene      
Name: nrfA    Texpresso search in the literature
Synonym(s): ECK4063, EG11781, b4070
Genome position(nucleotides): 4287764 --> 4289200 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.26
External database links:  
ASAP:
ABE-0013342
CGSC:
34336
ECHOBASE:
EB1729
ECOLIHUB:
nrfA
OU-MICROARRAY:
b4070
STRING:
511145.b4070
COLOMBOS: nrfA


Product      
Name: cytochrome c552 nitrite reductase
Synonym(s): NrfA, aeg-93, cytochrome c-552, cytochrome c552
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 53.703
Isoelectric point: 7.278
Motif(s):
 
Type Positions Sequence
1 -> 26 MTRIKINARRIFSLLIPFFFFTSVHA
43 -> 472 ETFAPQHPDQYLSWKATSEQSERVDALAEDPRLVILWAGYPFSRDYNKPRGHAFAVTDVRETLRTGAPKNAEDGPLPMACWSCKSPDVARLIQKDGEDGYFHGKWARGGPEIVNNLGCADCHNTASPEFAKGKPELTLSRPYAARAMEAIGKPFEKAGRFDQQSMVCGQCHVEYYFDGKNKAVKFPWDDGMKVENMEQYYDKIAFSDWTNSLSKTPMLKAQHPEYETWTAGIHGKNNVTCIDCHMPKVQNAEGKLYTDHKIGNPFDNFAQTCANCHTQDKAALQKVVAERKQSINDLKIKVEDQLVHAHFEAKAALDAGATEAEMKPIQDDIRHAQWRWDLAIASHGIHMHAPEEGLRMLGTAMDKAADARTKLARLLATKGITHEIQIPDISTKEKAQQAIGLNMEQIKAEKQDFIKTVIPQWEEQARK
126 -> 126 K
263 -> 263 Q
27 -> 478 EQTAAPAKPVTVEAKNETFAPQHPDQYLSWKATSEQSERVDALAEDPRLVILWAGYPFSRDYNKPRGHAFAVTDVRETLRTGAPKNAEDGPLPMACWSCKSPDVARLIQKDGEDGYFHGKWARGGPEIVNNLGCADCHNTASPEFAKGKPELTLSRPYAARAMEAIGKPFEKAGRFDQQSMVCGQCHVEYYFDGKNKAVKFPWDDGMKVENMEQYYDKIAFSDWTNSLSKTPMLKAQHPEYETWTAGIHGKNNVTCIDCHMPKVQNAEGKLYTDHKIGNPFDNFAQTCANCHTQDKAALQKVVAERKQSINDLKIKVEDQLVHAHFEAKAALDAGATEAEMKPIQDDIRHAQWRWDLAIASHGIHMHAPEEGLRMLGTAMDKAADARTKLARLLATKGITHEIQIPDISTKEKAQQAIGLNMEQIKAEKQDFIKTVIPQWEEQARKNGLLSQ

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
  1 - metabolism --> 1.4 - energy production/transport --> 1.4.2 - electron acceptors
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.15 - large molecule carriers --> 1.6.15.1 - cytochromes
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0005506 - iron ion binding
GO:0016966 - nitric oxide reductase activity
GO:0042279 - nitrite reductase (cytochrome, ammonia-forming) activity
GO:0005509 - calcium ion binding
GO:0020037 - heme binding
biological_process GO:0006807 - nitrogen compound metabolic process
GO:0019645 - anaerobic electron transport chain
GO:0042128 - nitrate assimilation
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
Reference(s): [1] Abou-Jaoude A., et al., 1977
[2] Abou-Jaoude A., et al., 1979
[3] Clarke TA., et al., 2008
[4] Clarke TA., et al., 2008
[5] Hussain H., et al., 1994
[6] Tyson K., et al., 1997
[7] Vine CE., et al., 2011
[8] Wang H., et al., 2000
[9] van Wonderen JH., et al., 2008
External database links:  
DIP:
DIP-36021N
ECOCYC:
CYTOCHROMEC552-MONOMER
ECOLIWIKI:
b4070
INTERPRO:
IPR017570
INTERPRO:
IPR011031
INTERPRO:
IPR003321
INTERPRO:
IPR036280
MODBASE:
P0ABK9
PANTHER:
PTHR30633
PDB:
4WJY
PDB:
3TOR
PDB:
3L1T
PDB:
2RF7
PDB:
2RDZ
PDB:
1GU6
PFAM:
PF02335
PRIDE:
P0ABK9
PRODB:
PRO_000023411
PROSITE:
PS51008
REFSEQ:
NP_418494
SMR:
P0ABK9
UNIPROT:
P0ABK9


Operon      
Name: nrfABCDEFG         
Operon arrangement:
Transcription unit        Promoter
nrfABCDEFG


Transcriptional Regulation      
Display Regulation             
Activated by: FNR, IHF, NarL, FlhDC, NarP
Repressed by: NsrR, IHF, NarL, 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| 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

[4] 

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



RNA cis-regulatory element    
Attenuation: Translational


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_4902 4287672 forward nd [RS-EPT-CBR] [10]


Evidence    

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



Reference(s)    

 [1] Abou-Jaoude A., Chippaux M., Pascal MC., Casse F., 1977, Formate : a new electron donor for nitrite reduction in Escherichia coli K12., Biochem Biophys Res Commun 78(2):579-83

 [2] Abou-Jaoude A., Pascal MC., Chippaux M., 1979, Formate-nitrite reduction in Escherichia coli K12. 2. Identification of components involved in the electron transfer., Eur J Biochem 95(2):315-21

 [3] Clarke TA., Kemp GL., Van Wonderen JH., Doyle RM., Cole JA., Tovell N., Cheesman MR., Butt JN., Richardson DJ., Hemmings AM., 2008, Role of a conserved glutamine residue in tuning the catalytic activity of Escherichia coli cytochrome c nitrite reductase., Biochemistry 47(12):3789-99

 [4] Clarke TA., Mills PC., Poock SR., Butt JN., Cheesman MR., Cole JA., Hinton JC., Hemmings AM., Kemp G., Soderberg CA., Spiro S., Van Wonderen J., Richardson DJ., 2008, Escherichia coli cytochrome c nitrite reductase NrfA., Methods Enzymol 437:63-77

 [5] Hussain H., Grove J., Griffiths L., Busby S., Cole J., 1994, A seven-gene operon essential for formate-dependent nitrite reduction to ammonia by enteric bacteria., Mol Microbiol 12(1):153-63

 [6] Tyson K., Metheringham R., Griffiths L., Cole J., 1997, Characterisation of Escherichia coli K-12 mutants defective in formate-dependent nitrite reduction: essential roles for hemN and the menFDBCE operon., Arch Microbiol 168(5):403-11

 [7] Vine CE., Purewal SK., Cole JA., 2011, NsrR-dependent method for detecting nitric oxide accumulation in the Escherichia coli cytoplasm and enzymes involved in NO production., FEMS Microbiol Lett 325(2):108-14

 [8] Wang H., Gunsalus RP., 2000, The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite., J Bacteriol 182(20):5813-22

 [9] van Wonderen JH., Burlat B., Richardson DJ., Cheesman MR., Butt JN., 2008, The nitric oxide reductase activity of cytochrome c nitrite reductase from Escherichia coli., J Biol Chem 283(15):9587-94

 [10] 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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