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Protein

Fumarate and nitrate reduction regulatory protein

Gene

fnr

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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.

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.

Cofactori

[4Fe-4S] clusterNote: Binds 1 [4Fe-4S] cluster per subunit.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi20Iron-sulfur (4Fe-4S)Sequence analysis1
Metal bindingi23Iron-sulfur (4Fe-4S)Sequence analysis1
Metal bindingi29Iron-sulfur (4Fe-4S)Sequence analysis1
Metal bindingi122Iron-sulfur (4Fe-4S)Sequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi197 – 216H-T-H motifPROSITE-ProRule annotationAdd BLAST20

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding Source: CollecTF
  • DNA binding Source: EcoCyc
  • DNA binding transcription factor activity Source: EcoCyc
  • iron-sulfur cluster binding Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • transcription regulatory region sequence-specific DNA binding Source: CollecTF

GO - Biological processi

  • anaerobic respiration Source: EcoCyc
  • positive regulation of transcription, DNA-templated Source: CollecTF
  • regulation of transcription, DNA-templated Source: EcoCyc
  • response to nitric oxide Source: EcoCyc
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionActivator, DNA-binding, Repressor
Biological processTranscription, Transcription regulation
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:PD00197

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10325 fnr

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • protein-DNA complex Source: CollecTF

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi16C → A: No effect. 1 Publication1
Mutagenesisi20C → S: Loss of activity. 1 Publication1
Mutagenesisi22D → G: Loss of regulation by O(2). 1 Publication1
Mutagenesisi23C → G: Loss of activity. 1 Publication1
Mutagenesisi28L → H: Loss of regulation by O(2). 1 Publication1
Mutagenesisi29C → G: Loss of activity. 1 Publication1
Mutagenesisi43D → G: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi64E → Q: No effect. 1 Publication1
Mutagenesisi72R → H: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi73S → F: Decrease in activity; no effect on DNA-binding. 2 Publications1
Mutagenesisi81I → T: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi82T → P: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi85G → A: Decrease in activity; no effect on DNA-binding. Trace activity; when associated with P-187. 2 Publications1
Mutagenesisi86D → A: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi87E → K: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi88Q → E: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi93H → R: Loss of regulation by O(2). 1 Publication1
Mutagenesisi96G → D: Loss of activity. 1 Publication1
Mutagenesisi118T → A or P: Decrease in activity; no effect on DNA-binding. 2 Publications1
Mutagenesisi120M → I, R, T or V: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi122C → A or S: Loss of activity. 1 Publication1
Mutagenesisi140R → A: Decrease in activity. 1
Mutagenesisi143M → A: Decrease in activity. 1
Mutagenesisi144M → A: Decrease in activity due to faulty dimerization. 1
Mutagenesisi145R → A: Decrease in activity. 1
Mutagenesisi146L → A: Decrease in activity. 1
Mutagenesisi147M → A: Decrease in activity due to faulty dimerization. 1
Mutagenesisi150E → K: Loss of regulation by O(2). 1 Publication1
Mutagenesisi151I → A: Decrease in activity due to faulty dimerization. 1
Mutagenesisi154D → A, G or V: Loss of regulation by O(2). 2 Publications1
Mutagenesisi158I → A: Decrease in activity due to faulty dimerization. 1
Mutagenesisi181F → L: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi186F → S: Decrease in activity; no effect on DNA-binding. 1 Publication1
Mutagenesisi187S → P: Decrease in activity; no effect on DNA-binding. Trace activity; when associated with A-85. 2 Publications1
Mutagenesisi191F → L: Decrease in activity; no effect on DNA-binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001001611 – 250Fumarate and nitrate reduction regulatory proteinAdd BLAST250

Proteomic databases

PaxDbiP0A9E5
PRIDEiP0A9E5

Expressioni

Gene expression databases

CollecTFiEXPREG_000007e0

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi4261852, 11 interactors
DIPiDIP-9669N
IntActiP0A9E5, 8 interactors
STRINGi316385.ECDH10B_1454

Structurei

3D structure databases

ProteinModelPortaliP0A9E5
SMRiP0A9E5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini164 – 237HTH crp-typePROSITE-ProRule annotationAdd BLAST74

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni20 – 29Essential for the oxygen-regulated activity10
Regioni47 – 50Activating region 2ASequence analysis4
Regioni60 – 61Activating region 3ASequence analysis2
Regioni71 – 75Activating region 1ASequence analysis5
Regioni81Activating region 3BSequence analysis1
Regioni85 – 87Activating region 3CSequence analysis3
Regioni112Activating region 3DSequence analysis1
Regioni116 – 121Activating region 1BSequence analysis6
Regioni123 – 124Activating region 2BSequence analysis2
Regioni127 – 128Activating region 2CSequence analysis2
Regioni140 – 159DimerizationSequence analysisAdd BLAST20
Regioni181 – 191Activating region 1CSequence analysisAdd BLAST11

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.

Phylogenomic databases

eggNOGiENOG4105DS0 Bacteria
COG0664 LUCA
HOGENOMiHOG000186461
InParanoidiP0A9E5
KOiK01420
OMAiAEVCVMP
PhylomeDBiP0A9E5

Family and domain databases

CDDicd00038 CAP_ED, 1 hit
Gene3Di1.10.10.10, 1 hit
2.60.120.10, 1 hit
InterProiView protein in InterPro
IPR018490 cNMP-bd-like
IPR000595 cNMP-bd_dom
IPR012318 HTH_CRP
IPR014710 RmlC-like_jellyroll
IPR018335 Tscrpt_reg_HTH_Crp-type_CS
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PfamiView protein in Pfam
PF00027 cNMP_binding, 1 hit
PF13545 HTH_Crp_2, 1 hit
PRINTSiPR00034 HTHCRP
SMARTiView protein in SMART
SM00100 cNMP, 1 hit
SM00419 HTH_CRP, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
SSF51206 SSF51206, 1 hit
PROSITEiView protein in PROSITE
PS50042 CNMP_BINDING_3, 1 hit
PS00042 HTH_CRP_1, 1 hit
PS51063 HTH_CRP_2, 1 hit

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:
EMBLi
GenBanki
DDBJi
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
WP_000611911.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC74416; AAC74416; b1334
BAA14927; BAA14927; BAA14927
GeneIDi945908
KEGGiecj:JW1328
eco:b1334
PATRICifig|1411691.4.peg.943

Similar proteinsi

Entry informationi

Entry nameiFNR_ECOLI
AccessioniPrimary (citable) accession number: P0A9E5
Secondary accession number(s): P03019
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 19, 2005
Last modified: March 28, 2018
This is version 105 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene

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