RegulonDB RegulonDB 10.8: Gene Form
   

fnr gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

uspE fnr ogt IHF FNR ppGpp fnrp fnrp uspEp uspEp TSS_1758 TSS_1758

Gene      
Name: fnr    Texpresso search in the literature
Synonym(s): ECK1330, EG10325, b1334, nirA, nirR, ossA, oxrA
Genome position(nucleotides): 1398774 <-- 1399526 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.66
External database links:  
ASAP:
ABE-0004475
CGSC:
745
ECHOBASE:
EB0321
OU-MICROARRAY:
b1334
PortEco:
fnr
STRING:
511145.b1334
COLOMBOS: fnr


Product      
Name: DNA-binding transcriptional dual regulator FNR
Synonym(s): Fnr, NirA, NirR, OssA, OxrA
Sequence: Get amino acid sequence Fasta Format
Regulator Family: CRP
Cellular location: cytosol
Molecular weight: 27.967
Isoelectric point: 8.214
Motif(s):
 
Type Positions Sequence
29 -> 29 C
51 -> 132 PIQKGQTLFKAGDELKSLYAIRSGTIKSYTITEQGDEQITGFHLAGDLVGFDAIGSGHHPSFAQALETSMVCEIPFETLDDL
96 -> 96 G
123 -> 124 EI
127 -> 128 ET

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.4 - global
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0032993 - protein-DNA complex
molecular_function GO:0003677 - DNA binding
GO:0046872 - metal ion binding
GO:0003700 - DNA-binding transcription factor activity
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0000976 - transcription regulatory region sequence-specific DNA binding
GO:0001216 - DNA-binding transcription activator activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0009061 - anaerobic respiration
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0071731 - response to nitric oxide
Evidence: [AIFS] Automated inference of function from sequence
[APPHINH] Assay of protein purified to homogeneity from its native host
[APPINH] Assay of protein partially-purified from its native host
[HIFS] Human inference of function from sequence
Reference(s): [1] Eiglmeier K., et al., 1989
[2] Gerasimova AV., et al., 2001
[3] Green J., et al., 2001
[4] Iuchi S., et al., 1993
[5] Kiley PJ., et al., 1998
[6] Lambden PR., et al., 1976
[7] Mettert EL., et al., 2007
[8] Rouault TA., et al., 1996
[9] Shaw DJ., et al., 1982
[10] Spiro S. 1994
[11] Spiro S., et al., 1991
[12] Spiro S., et al., 1990
[13] Takahashi K., et al., 1994
[14] Trageser M., et al., 1990
[15] Unden G., et al., 2002
[16] Unden G., et al., 1995
[17] Unden G., et al., 1997
[18] Unden G., et al., 1997
[19] Unden G., et al., 1991
External database links:  
DIP:
DIP-9669N
ECOCYC:
PD00197
ECOLIWIKI:
b1334
INTERPRO:
IPR014710
INTERPRO:
IPR036390
INTERPRO:
IPR036388
INTERPRO:
IPR018490
INTERPRO:
IPR018335
INTERPRO:
IPR012318
INTERPRO:
IPR000595
MINT:
MINT-1237977
MODBASE:
P0A9E5
PFAM:
PF00027
PFAM:
PF13545
PRIDE:
P0A9E5
PRINTS:
PR00034
PRODB:
PRO_000022676
PROSITE:
PS00042
PROSITE:
PS51063
PROSITE:
PS50042
REFSEQ:
NP_415850
SMART:
SM00100
SMART:
SM00419
SMR:
P0A9E5
UNIPROT:
P0A9E5


Operon      
Name: fnr         
Operon arrangement:
Transcription unit        Promoter
fnr


Transcriptional Regulation      
Display Regulation             
Activated by: IHF
Repressed by: FNR, Fur, ArcA


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_1758 1398266 forward nd [RS-EPT-CBR] [20]


Evidence    

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



Reference(s)    

 [1] Eiglmeier K., Honore N., Iuchi S., Lin EC., Cole ST., 1989, Molecular genetic analysis of FNR-dependent promoters., Mol Microbiol 3(7):869-78

 [2] Gerasimova AV., Rodionov DA., Mironov AA., Gel'fand MS., 2001, [Computer analysis of regulatory signals in bacterial genomes. Fnr binding segments], Mol Biol (Mosk) 35(6):1001-9

 [3] Green J., Scott C., Guest JR., 2001, Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP., Adv Microb Physiol 44:1-34

 [4] Iuchi S., Lin EC., 1993, Adaptation of Escherichia coli to redox environments by gene expression., Mol Microbiol 9(1):9-15

 [5] Kiley PJ., Beinert H., 1998, Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster., FEMS Microbiol Rev 22(5):341-52

 [6] Lambden PR., Guest JR., 1976, Mutants of Escherichia coli K12 unable to use fumarate as an anaerobic electron acceptor., J Gen Microbiol 97(2):145-60

 [7] Mettert EL., Kiley PJ., 2007, Contributions of [4Fe-4S]-FNR and integration host factor to fnr transcriptional regulation., J Bacteriol 189(8):3036-43

 [8] Rouault TA., Klausner RD., 1996, Iron-sulfur clusters as biosensors of oxidants and iron., Trends Biochem Sci 21(5):174-7

 [9] Shaw DJ., Guest JR., 1982, Nucleotide sequence of the fnr gene and primary structure of the Enr protein of Escherichia coli., Nucleic Acids Res 10(19):6119-30

 [10] Spiro S., 1994, The FNR family of transcriptional regulators., Antonie Van Leeuwenhoek 66(1-3):23-36

 [11] Spiro S., Guest JR., 1991, Adaptive responses to oxygen limitation in Escherichia coli., Trends Biochem Sci 16(8):310-4

 [12] Spiro S., Guest JR., 1990, FNR and its role in oxygen-regulated gene expression in Escherichia coli., FEMS Microbiol Rev 6(4):399-428

 [13] Takahashi K., Hattori T., Nakanishi T., Nohno T., Fujita N., Ishihama A., Taniguchi S., 1994, Repression of in vitro transcription of the Escherichia coli fnr and nar X genes by FNR protein., FEBS Lett 340(1-2):59-64

 [14] Trageser M., Spiro S., Duchene A., Kojro E., Fahrenholz F., Guest JR., Unden G., 1990, Isolation of intact FNR protein (Mr 30,000) of Escherichia coli., Mol Microbiol 4(1):21-7

 [15] Unden G., Achebach S., Holighaus G., Tran HG., Wackwitz B., Zeuner Y., 2002, Control of FNR function of Escherichia coli by O2 and reducing conditions., J Mol Microbiol Biotechnol 4(3):263-8

 [16] Unden G., Becker S., Bongaerts J., Holighaus G., Schirawski J., Six S., 1995, O2-sensing and O2-dependent gene regulation in facultatively anaerobic bacteria., Arch Microbiol 164(2):81-90

 [17] Unden G., Bongaerts J., 1997, Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors., Biochim Biophys Acta 1320(3):217-34

 [18] Unden G., Schirawski J., 1997, The oxygen-responsive transcriptional regulator FNR of Escherichia coli: the search for signals and reactions., Mol Microbiol 25(2):205-10

 [19] Unden G., Trageser M., 1991, Oxygen regulated gene expression in Escherichia coli: control of anaerobic respiration by the FNR protein., Antonie Van Leeuwenhoek 59(2):65-76

 [20] 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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