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P0A9E5

- FNR_ECOLI

UniProt

P0A9E5 - FNR_ECOLI

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Protein

Fumarate and nitrate reduction regulatory protein

Gene

fnr

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Global transcription factor that controls the expression of over 100 target genes in response to anoxia. It facilitates the adaptation to anaerobic growth conditions by regulating the expression of gene products that are involved in anaerobic energy metabolism. When the terminal electron acceptor, O2, is no longer available, it represses the synthesis of enzymes involved in aerobic respiration and increases the synthesis of enzymes required for anaerobic respiration.

Cofactori

Binds 1 4Fe-4S cluster per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi20 – 201Iron-sulfur (4Fe-4S)Sequence Analysis
Metal bindingi23 – 231Iron-sulfur (4Fe-4S)Sequence Analysis
Metal bindingi29 – 291Iron-sulfur (4Fe-4S)Sequence Analysis
Metal bindingi122 – 1221Iron-sulfur (4Fe-4S)Sequence Analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi197 – 21620H-T-H motifPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: EcoCyc
  2. DNA binding Source: EcoCyc
  3. iron-sulfur cluster binding Source: EcoCyc
  4. metal ion binding Source: UniProtKB-KW
  5. sequence-specific DNA binding transcription factor activity Source: EcoCyc

GO - Biological processi

  1. anaerobic respiration Source: EcoCyc
  2. regulation of transcription, DNA-templated Source: EcoCyc
  3. response to nitric oxide Source: EcoCyc
  4. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

4Fe-4S, DNA-binding, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:PD00197.
ECOL316407:JW1328-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Fumarate and nitrate reduction regulatory protein
Gene namesi
Name:fnr
Synonyms:nirR
Ordered Locus Names:b1334, JW1328
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10325. fnr.

Subcellular locationi

Cytoplasm Curated

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi16 – 161C → A: No effect. 1 Publication
Mutagenesisi20 – 201C → S: Loss of activity. 1 Publication
Mutagenesisi22 – 221D → G: Loss of regulation by O(2). 1 Publication
Mutagenesisi23 – 231C → G: Loss of activity. 1 Publication
Mutagenesisi28 – 281L → H: Loss of regulation by O(2). 1 Publication
Mutagenesisi29 – 291C → G: Loss of activity. 1 Publication
Mutagenesisi43 – 431D → G: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi64 – 641E → Q: No effect. 1 Publication
Mutagenesisi72 – 721R → H: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi73 – 731S → F: Decrease in activity; no effect on DNA-binding. 2 Publications
Mutagenesisi81 – 811I → T: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi82 – 821T → P: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi85 – 851G → A: Decrease in activity; no effect on DNA-binding. Trace activity; when associated with P-187. 2 Publications
Mutagenesisi86 – 861D → A: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi87 – 871E → K: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi88 – 881Q → E: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi93 – 931H → R: Loss of regulation by O(2). 1 Publication
Mutagenesisi96 – 961G → D: Loss of activity. 1 Publication
Mutagenesisi118 – 1181T → A or P: Decrease in activity; no effect on DNA-binding. 2 Publications
Mutagenesisi120 – 1201M → I, R, T or V: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi122 – 1221C → A or S: Loss of activity. 1 Publication
Mutagenesisi140 – 1401R → A: Decrease in activity.
Mutagenesisi143 – 1431M → A: Decrease in activity.
Mutagenesisi144 – 1441M → A: Decrease in activity due to faulty dimerization.
Mutagenesisi145 – 1451R → A: Decrease in activity.
Mutagenesisi146 – 1461L → A: Decrease in activity.
Mutagenesisi147 – 1471M → A: Decrease in activity due to faulty dimerization.
Mutagenesisi150 – 1501E → K: Loss of regulation by O(2). 1 Publication
Mutagenesisi151 – 1511I → A: Decrease in activity due to faulty dimerization.
Mutagenesisi154 – 1541D → A, G or V: Loss of regulation by O(2). 2 Publications
Mutagenesisi158 – 1581I → A: Decrease in activity due to faulty dimerization.
Mutagenesisi181 – 1811F → L: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi186 – 1861F → S: Decrease in activity; no effect on DNA-binding. 1 Publication
Mutagenesisi187 – 1871S → P: Decrease in activity; no effect on DNA-binding. Trace activity; when associated with A-85. 2 Publications
Mutagenesisi191 – 1911F → L: Decrease in activity; no effect on DNA-binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 250250Fumarate and nitrate reduction regulatory proteinPRO_0000100161Add
BLAST

Proteomic databases

PaxDbiP0A9E5.
PRIDEiP0A9E5.

Expressioni

Gene expression databases

GenevestigatoriP0A9E5.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

DIPiDIP-9669N.
IntActiP0A9E5. 8 interactions.
MINTiMINT-1237977.
STRINGi511145.b1334.

Structurei

3D structure databases

ProteinModelPortaliP0A9E5.
SMRiP0A9E5. Positions 53-242.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini164 – 23774HTH crp-typePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni20 – 2910Essential for the oxygen-regulated activity
Regioni47 – 504Activating region 2ASequence Analysis
Regioni60 – 612Activating region 3ASequence Analysis
Regioni71 – 755Activating region 1ASequence Analysis
Regioni81 – 811Activating region 3BSequence Analysis
Regioni85 – 873Activating region 3CSequence Analysis
Regioni112 – 1121Activating region 3DSequence Analysis
Regioni116 – 1216Activating region 1BSequence Analysis
Regioni123 – 1242Activating region 2BSequence Analysis
Regioni127 – 1282Activating region 2CSequence Analysis
Regioni140 – 15920DimerizationSequence AnalysisAdd
BLAST
Regioni181 – 19111Activating region 1CSequence AnalysisAdd
BLAST

Domaini

The amino acid residues contacting the FNR target site on the DNA (5'-TTGATNNNNATCAA-3') are located in the putative DNA-recognition helix (alphaF), which contains the FNR motif (EXXSR). Three surface-exposed loops forming activating region 1 (AR1) in the downstream subunit of the dimer contact the C-terminal domain of the alpha subunit (alphaCTD) of RNA polymerase for activation of class I promoters (the 161-121 loop is the major AR1 activating determinant). At class II promoters, the AR1 of the upstream subunit contacts alphaCTD, promoting open complex formation; activating region 3 (AR3) of the downstream subunit contacts region 4 of the sigma70 subunit of RNA polymerase, to effect direct activation. At promoters repressed by FNR, tandem FNR dimers might interact with each other at AR1 to restrict access to a promoter or jam the promoter by their dual interaction with RNA polymerase alphaCTD.

Sequence similaritiesi

Contains 1 cyclic nucleotide-binding domain.PROSITE-ProRule annotation
Contains 1 HTH crp-type DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0664.
HOGENOMiHOG000186461.
InParanoidiP0A9E5.
KOiK01420.
OMAiFSANQFR.
OrthoDBiEOG6RVFWF.
PhylomeDBiP0A9E5.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
2.60.120.10. 1 hit.
InterProiIPR018490. cNMP-bd-like.
IPR000595. cNMP-bd_dom.
IPR012318. HTH_CRP_2.
IPR014710. RmlC-like_jellyroll.
IPR001808. Tscrpt_reg_HTH_Crp.
IPR018335. Tscrpt_reg_HTH_Crp-type_CS.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00027. cNMP_binding. 1 hit.
PF00325. Crp. 1 hit.
[Graphical view]
PRINTSiPR00034. HTHCRP.
SMARTiSM00100. cNMP. 1 hit.
SM00419. HTH_CRP. 1 hit.
[Graphical view]
SUPFAMiSSF51206. SSF51206. 1 hit.
PROSITEiPS50042. CNMP_BINDING_3. 1 hit.
PS00042. HTH_CRP_1. 1 hit.
PS51063. HTH_CRP_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A9E5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIPEKRIIRR IQSGGCAIHC QDCSISQLCI PFTLNEHELD QLDNIIERKK
60 70 80 90 100
PIQKGQTLFK AGDELKSLYA IRSGTIKSYT ITEQGDEQIT GFHLAGDLVG
110 120 130 140 150
FDAIGSGHHP SFAQALETSM VCEIPFETLD DLSGKMPNLR QQMMRLMSGE
160 170 180 190 200
IKGDQDMILL LSKKNAEERL AAFIYNLSRR FAQRGFSPRE FRLTMTRGDI
210 220 230 240 250
GNYLGLTVET ISRLLGRFQK SGMLAVKGKY ITIENNDALA QLAGHTRNVA
Length:250
Mass (Da):27,967
Last modified:July 19, 2005 - v1
Checksum:i33F7BFA2972FF703
GO

Mass spectrometryi

Molecular mass is 26823±6 Da from positions 10 - 250. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J01608 Genomic DNA. Translation: AAA87981.1. Sequence problems.
U00096 Genomic DNA. Translation: AAC74416.1.
AP009048 Genomic DNA. Translation: BAA14927.1.
PIRiA64883. RGECF.
RefSeqiNP_415850.1. NC_000913.3.
YP_489604.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74416; AAC74416; b1334.
BAA14927; BAA14927; BAA14927.
GeneIDi12932858.
945908.
KEGGiecj:Y75_p1311.
eco:b1334.
PATRICi32117944. VBIEscCol129921_1392.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J01608 Genomic DNA. Translation: AAA87981.1 . Sequence problems.
U00096 Genomic DNA. Translation: AAC74416.1 .
AP009048 Genomic DNA. Translation: BAA14927.1 .
PIRi A64883. RGECF.
RefSeqi NP_415850.1. NC_000913.3.
YP_489604.1. NC_007779.1.

3D structure databases

ProteinModelPortali P0A9E5.
SMRi P0A9E5. Positions 53-242.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9669N.
IntActi P0A9E5. 8 interactions.
MINTi MINT-1237977.
STRINGi 511145.b1334.

Proteomic databases

PaxDbi P0A9E5.
PRIDEi P0A9E5.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74416 ; AAC74416 ; b1334 .
BAA14927 ; BAA14927 ; BAA14927 .
GeneIDi 12932858.
945908.
KEGGi ecj:Y75_p1311.
eco:b1334.
PATRICi 32117944. VBIEscCol129921_1392.

Organism-specific databases

EchoBASEi EB0321.
EcoGenei EG10325. fnr.

Phylogenomic databases

eggNOGi COG0664.
HOGENOMi HOG000186461.
InParanoidi P0A9E5.
KOi K01420.
OMAi FSANQFR.
OrthoDBi EOG6RVFWF.
PhylomeDBi P0A9E5.

Enzyme and pathway databases

BioCyci EcoCyc:PD00197.
ECOL316407:JW1328-MONOMER.

Miscellaneous databases

PROi P0A9E5.

Gene expression databases

Genevestigatori P0A9E5.

Family and domain databases

Gene3Di 1.10.10.10. 1 hit.
2.60.120.10. 1 hit.
InterProi IPR018490. cNMP-bd-like.
IPR000595. cNMP-bd_dom.
IPR012318. HTH_CRP_2.
IPR014710. RmlC-like_jellyroll.
IPR001808. Tscrpt_reg_HTH_Crp.
IPR018335. Tscrpt_reg_HTH_Crp-type_CS.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view ]
Pfami PF00027. cNMP_binding. 1 hit.
PF00325. Crp. 1 hit.
[Graphical view ]
PRINTSi PR00034. HTHCRP.
SMARTi SM00100. cNMP. 1 hit.
SM00419. HTH_CRP. 1 hit.
[Graphical view ]
SUPFAMi SSF51206. SSF51206. 1 hit.
PROSITEi PS50042. CNMP_BINDING_3. 1 hit.
PS00042. HTH_CRP_1. 1 hit.
PS51063. HTH_CRP_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the fnr gene and primary structure of the Enr protein of Escherichia coli."
    Shaw D.J., Guest J.R.
    Nucleic Acids Res. 10:6119-6130(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Isolation of intact FNR protein (Mr 30,000) of Escherichia coli."
    Trageser M., Spiro S., Duchene A., Kojro E., Fahrenholz F., Guest J.R., Unden G.
    Mol. Microbiol. 4:21-27(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-19, SEQUENCE REVISION TO 29.
  6. "The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state."
    Lazazzera B.A., Bates D.M., Kiley P.J.
    Genes Dev. 7:1993-2005(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, MUTAGENESIS OF ASP-154.
    Strain: K12 / MG1655 / ATCC 47076.
  7. "Iron-sulfur cluster disassembly in the FNR protein of Escherichia coli by O2: [4Fe-4S] to [2Fe-2S] conversion with loss of biological activity."
    Khoroshilova N., Popescu C., Muenck E., Beinert H., Kiley P.J.
    Proc. Natl. Acad. Sci. U.S.A. 94:6087-6092(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
    Strain: B.
  8. "Anaerobic acquisition of [4FE 4S] clusters by the inactive FNR(C20S) variant and restoration of activity by second-site amino acid substitutions."
    Ralph E.T., Scott C., Jordan P.A., Thomson A.J., Guest J.R., Green J.
    Mol. Microbiol. 39:1199-1211(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, MUTAGENESIS.
  9. "Properties of FNR proteins substituted at each of the five cysteine residues."
    Green J., Sharrocks A.D., Green B., Geisow M., Guest J.R.
    Mol. Microbiol. 8:61-68(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: MASS SPECTROMETRY, CHARACTERIZATION OF MUTANTS.
  10. "In vivo and in vitro mutants of FNR the anaerobic transcriptional regulator of E. coli."
    Sharrocks A.D., Green J., Guest J.R.
    FEBS Lett. 270:119-122(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-16; CYS-20; CYS-23; CYS-29; GLU-64; GLY-96 AND CYS-122.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  11. "Fnr mutants that activate gene expression in the presence of oxygen."
    Kiley P.J., Reznikoff W.S.
    J. Bacteriol. 173:16-22(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-22; LEU-28; HIS-93; GLU-150 AND ASP-154.
    Strain: K12 / MG1655 / ATCC 47076.
  12. "The role of two surface exposed loops in transcription activation by the Escherichia coli CRP and FNR proteins."
    Williams R., Bell A., Sims G., Busby S.J.W.
    Nucleic Acids Res. 19:6705-6712(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ILE-81; THR-82; GLY-85; ASP-86; GLU-87 AND GLN-88.
  13. "Transcription activation at class I FNR-dependent promoters: identification of the activating surface of FNR and the corresponding contact site in the C-terminal domain of the RNA polymerase alpha subunit."
    Williams S.M., Savery N.J., Busby S.J.W., Wing H.J.
    Nucleic Acids Res. 25:4028-4034(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-43; ARG-72; SER-73; GLY-74; THR-118; MET-120; PHE-181; PHE-186; SER-187 AND PHE-191.
  14. "FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3."
    Lamberg K.E., Kiley P.J.
    Mol. Microbiol. 38:817-827(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF SER-73; GLY-85; THR-118 AND SER-187.
    Strain: K12 / MG1655 / ATCC 47076.
  15. "Characterization of the dimerization domain in the FNR transcription factor."
    Moore L.J., Kiley P.J.
    J. Biol. Chem. 276:45744-45750(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ALL RESIDUES IN THE DIMERIZATION HELIX.
    Strain: K12 / MG1655 / ATCC 47076.
  16. "FNR and its role in oxygen-regulated gene expression in Escherichia coli."
    Spiro S., Guest J.R.
    FEMS Microbiol. Rev. 6:399-428(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  17. "Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster."
    Kiley P.J., Beinert H.
    FEMS Microbiol. Rev. 22:341-352(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  18. "Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP."
    Green J., Scott C., Guest J.R.
    Adv. Microb. Physiol. 44:1-34(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.

Entry informationi

Entry nameiFNR_ECOLI
AccessioniPrimary (citable) accession number: P0A9E5
Secondary accession number(s): P03019
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 19, 2005
Last modified: October 29, 2014
This is version 82 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

FNR senses the oxygen concentration directly via the disassembly and reassembly of the [4Fe-4S] clusters. Anaerobic, de novo acquisition of the iron-sulfur cluster converts monomeric, inactive apo-FNR into a dimeric form containing two [4Fe-4S] clusters. This, in turn, enhances the affinity of FNR for specific DNA targets and mediates transcription regulation by establishing direct FNR-RNA polymerase contacts. With the increase in intracellular oxygen concentration, the [4Fe-4S] cluster is oxidized, producing a [2Fe-2S] cluster, which decays to apo-FNR. Apo-FNR [4SH] can be reversibly oxidized to a disulfide form [2SH,S-S], suggesting that FNR may be able to sense oxidative stress as well as normoxia. This interconversion may be mediated by agents such as glutathione or thioredoxin.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3