ID FNR_ECOLI Reviewed; 250 AA. AC P0A9E5; P03019; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 19-JUL-2005, sequence version 1. DT 14-DEC-2022, entry version 130. DE RecName: Full=Fumarate and nitrate reduction regulatory protein; GN Name=fnr; Synonyms=nirR; OrderedLocusNames=b1334, JW1328; OS Escherichia coli (strain K12). OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=6292868; DOI=10.1093/nar/10.19.6119; RA Shaw D.J., Guest J.R.; RT "Nucleotide sequence of the fnr gene and primary structure of the Enr RT protein of Escherichia coli."; RL Nucleic Acids Res. 10:6119-6130(1982). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=9097039; DOI=10.1093/dnares/3.6.363; RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., RA Wada C., Yamamoto Y., Horiuchi T.; RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to RT the 28.0-40.1 min region on the linkage map."; RL DNA Res. 3:363-377(1996). RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=9278503; DOI=10.1126/science.277.5331.1453; RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., RA Shao Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1462(1997). RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=16738553; DOI=10.1038/msb4100049; RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.; RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 RT and W3110."; RL Mol. Syst. Biol. 2:E1-E5(2006). RN [5] RP PROTEIN SEQUENCE OF 1-19, AND SEQUENCE REVISION TO 29. RX PubMed=2181237; DOI=10.1111/j.1365-2958.1990.tb02011.x; RA Trageser M., Spiro S., Duchene A., Kojro E., Fahrenholz F., Guest J.R., RA Unden G.; RT "Isolation of intact FNR protein (Mr 30,000) of Escherichia coli."; RL Mol. Microbiol. 4:21-27(1990). RN [6] RP CHARACTERIZATION, AND MUTAGENESIS OF ASP-154. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=8406003; DOI=10.1101/gad.7.10.1993; RA Lazazzera B.A., Bates D.M., Kiley P.J.; RT "The activity of the Escherichia coli transcription factor FNR is regulated RT by a change in oligomeric state."; RL Genes Dev. 7:1993-2005(1993). RN [7] RP CHARACTERIZATION. RC STRAIN=B; RX PubMed=9177174; DOI=10.1073/pnas.94.12.6087; RA Khoroshilova N., Popescu C., Muenck E., Beinert H., Kiley P.J.; RT "Iron-sulfur cluster disassembly in the FNR protein of Escherichia coli by RT O2: [4Fe-4S] to [2Fe-2S] conversion with loss of biological activity."; RL Proc. Natl. Acad. Sci. U.S.A. 94:6087-6092(1997). RN [8] RP CHARACTERIZATION, AND MUTAGENESIS. RX PubMed=11251837; DOI=10.1111/j.1365-2958.2001.02326.x; RA Ralph E.T., Scott C., Jordan P.A., Thomson A.J., Guest J.R., Green J.; RT "Anaerobic acquisition of [4FE 4S] clusters by the inactive FNR(C20S) RT variant and restoration of activity by second-site amino acid RT substitutions."; RL Mol. Microbiol. 39:1199-1211(2001). RN [9] RP MASS SPECTROMETRY, AND CHARACTERIZATION OF MUTANTS. RX PubMed=8497198; DOI=10.1111/j.1365-2958.1993.tb01203.x; RA Green J., Sharrocks A.D., Green B., Geisow M., Guest J.R.; RT "Properties of FNR proteins substituted at each of the five cysteine RT residues."; RL Mol. Microbiol. 8:61-68(1993). RN [10] RP MUTAGENESIS OF CYS-16; CYS-20; CYS-23; CYS-29; GLU-64; GLY-96 AND CYS-122. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=2226775; DOI=10.1016/0014-5793(90)81248-m; RA Sharrocks A.D., Green J., Guest J.R.; RT "In vivo and in vitro mutants of FNR the anaerobic transcriptional RT regulator of E. coli."; RL FEBS Lett. 270:119-122(1990). RN [11] RP MUTAGENESIS OF ASP-22; LEU-28; HIS-93; GLU-150 AND ASP-154. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=1898918; DOI=10.1128/jb.173.1.16-22.1991; RA Kiley P.J., Reznikoff W.S.; RT "Fnr mutants that activate gene expression in the presence of oxygen."; RL J. Bacteriol. 173:16-22(1991). RN [12] RP MUTAGENESIS OF ILE-81; THR-82; GLY-85; ASP-86; GLU-87 AND GLN-88. RX PubMed=1762901; DOI=10.1093/nar/19.24.6705; RA Williams R., Bell A., Sims G., Busby S.J.W.; RT "The role of two surface exposed loops in transcription activation by the RT Escherichia coli CRP and FNR proteins."; RL Nucleic Acids Res. 19:6705-6712(1991). RN [13] RP MUTAGENESIS OF ASP-43; ARG-72; SER-73; GLY-74; THR-118; MET-120; PHE-181; RP PHE-186; SER-187 AND PHE-191. RX PubMed=9321653; DOI=10.1093/nar/25.20.4028; RA Williams S.M., Savery N.J., Busby S.J.W., Wing H.J.; RT "Transcription activation at class I FNR-dependent promoters: RT identification of the activating surface of FNR and the corresponding RT contact site in the C-terminal domain of the RNA polymerase alpha RT subunit."; RL Nucleic Acids Res. 25:4028-4034(1997). RN [14] RP MUTAGENESIS OF SER-73; GLY-85; THR-118 AND SER-187. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=11115116; DOI=10.1046/j.1365-2958.2000.02172.x; RA Lamberg K.E., Kiley P.J.; RT "FNR-dependent activation of the class II dmsA and narG promoters of RT Escherichia coli requires FNR-activating regions 1 and 3."; RL Mol. Microbiol. 38:817-827(2000). RN [15] RP MUTAGENESIS OF ALL RESIDUES IN THE DIMERIZATION HELIX. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=11581261; DOI=10.1074/jbc.m106569200; RA Moore L.J., Kiley P.J.; RT "Characterization of the dimerization domain in the FNR transcription RT factor."; RL J. Biol. Chem. 276:45744-45750(2001). RN [16] RP REVIEW. RX PubMed=2248796; DOI=10.1111/j.1574-6968.1990.tb04109.x; RA Spiro S., Guest J.R.; RT "FNR and its role in oxygen-regulated gene expression in Escherichia RT coli."; RL FEMS Microbiol. Rev. 6:399-428(1990). RN [17] RP REVIEW. RX PubMed=9990723; DOI=10.1111/j.1574-6976.1998.tb00375.x; RA Kiley P.J., Beinert H.; RT "Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur RT cluster."; RL FEMS Microbiol. Rev. 22:341-352(1998). RN [18] RP REVIEW. RX PubMed=11407111; DOI=10.1016/s0065-2911(01)44010-0; RA Green J., Scott C., Guest J.R.; RT "Functional versatility in the CRP-FNR superfamily of transcription RT factors: FNR and FLP."; RL Adv. Microb. Physiol. 44:1-34(2001). CC -!- FUNCTION: Global transcription factor that controls the expression of CC over 100 target genes in response to anoxia. It facilitates the CC adaptation to anaerobic growth conditions by regulating the expression CC of gene products that are involved in anaerobic energy metabolism. When CC the terminal electron acceptor, O(2), is no longer available, it CC represses the synthesis of enzymes involved in aerobic respiration and CC increases the synthesis of enzymes required for anaerobic respiration. CC -!- COFACTOR: CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; CC Note=Binds 1 [4Fe-4S] cluster per subunit.; CC -!- SUBUNIT: Homodimer. CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}. CC -!- DOMAIN: The amino acid residues contacting the FNR target site on the CC DNA (5'-TTGATNNNNATCAA-3') are located in the putative DNA-recognition CC helix (alphaF), which contains the FNR motif (EXXSR). Three surface- CC exposed loops forming activating region 1 (AR1) in the downstream CC subunit of the dimer contact the C-terminal domain of the alpha subunit CC (alphaCTD) of RNA polymerase for activation of class I promoters (the CC 161-121 loop is the major AR1 activating determinant). At class II CC promoters, the AR1 of the upstream subunit contacts alphaCTD, promoting CC open complex formation; activating region 3 (AR3) of the downstream CC subunit contacts region 4 of the sigma70 subunit of RNA polymerase, to CC effect direct activation. At promoters repressed by FNR, tandem FNR CC dimers might interact with each other at AR1 to restrict access to a CC promoter or jam the promoter by their dual interaction with RNA CC polymerase alphaCTD. CC -!- MASS SPECTROMETRY: Mass=26823; Mass_error=6; Method=Electrospray; CC Evidence={ECO:0000269|PubMed:8497198}; CC -!- MISCELLANEOUS: FNR senses the oxygen concentration directly via the CC disassembly and reassembly of the [4Fe-4S] clusters. Anaerobic, de novo CC acquisition of the iron-sulfur cluster converts monomeric, inactive CC apo-FNR into a dimeric form containing two [4Fe-4S] clusters. This, in CC turn, enhances the affinity of FNR for specific DNA targets and CC mediates transcription regulation by establishing direct FNR-RNA CC polymerase contacts. With the increase in intracellular oxygen CC concentration, the [4Fe-4S] cluster is oxidized, producing a [2Fe-2S] CC cluster, which decays to apo-FNR. Apo-FNR [4SH] can be reversibly CC oxidized to a disulfide form [2SH,S-S], suggesting that FNR may be able CC to sense oxidative stress as well as normoxia. This interconversion may CC be mediated by agents such as glutathione or thioredoxin. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; J01608; AAA87981.1; ALT_SEQ; Genomic_DNA. DR EMBL; U00096; AAC74416.1; -; Genomic_DNA. DR EMBL; AP009048; BAA14927.1; -; Genomic_DNA. DR PIR; A64883; RGECF. DR RefSeq; NP_415850.1; NC_000913.3. DR RefSeq; WP_000611911.1; NZ_STEB01000005.1. DR AlphaFoldDB; P0A9E5; -. DR SMR; P0A9E5; -. DR BioGRID; 4261852; 108. DR BioGRID; 850273; 2. DR DIP; DIP-9669N; -. DR IntAct; P0A9E5; 8. DR STRING; 511145.b1334; -. DR jPOST; P0A9E5; -. DR PaxDb; P0A9E5; -. DR EnsemblBacteria; AAC74416; AAC74416; b1334. DR EnsemblBacteria; BAA14927; BAA14927; BAA14927. DR GeneID; 66674838; -. DR GeneID; 945908; -. DR KEGG; ecj:JW1328; -. DR KEGG; eco:b1334; -. DR PATRIC; fig|1411691.4.peg.943; -. DR EchoBASE; EB0321; -. DR eggNOG; COG0664; Bacteria. DR HOGENOM; CLU_075053_0_2_6; -. DR InParanoid; P0A9E5; -. DR OMA; AEVCVMP; -. DR PhylomeDB; P0A9E5; -. DR BioCyc; EcoCyc:PD00197; -. DR PHI-base; PHI:4876; -. DR PHI-base; PHI:7248; -. DR PRO; PR:P0A9E5; -. DR Proteomes; UP000000318; Chromosome. DR Proteomes; UP000000625; Chromosome. DR CollecTF; EXPREG_000007e0; -. DR GO; GO:0005829; C:cytosol; IDA:EcoCyc. DR GO; GO:0032993; C:protein-DNA complex; IMP:CollecTF. DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc. DR GO; GO:0003677; F:DNA binding; IDA:EcoCyc. DR GO; GO:0001216; F:DNA-binding transcription activator activity; IMP:CollecTF. DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:EcoCyc. DR GO; GO:0051536; F:iron-sulfur cluster binding; IDA:EcoCyc. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0000976; F:transcription cis-regulatory region binding; IMP:CollecTF. DR GO; GO:0009061; P:anaerobic respiration; IEP:EcoCyc. DR GO; GO:0045893; P:positive regulation of DNA-templated transcription; IDA:CollecTF. DR GO; GO:0006355; P:regulation of DNA-templated transcription; IEP:EcoCyc. DR GO; GO:0071731; P:response to nitric oxide; IEP:EcoCyc. DR CDD; cd00038; CAP_ED; 1. DR Gene3D; 1.10.10.10; -; 1. DR Gene3D; 2.60.120.10; -; 1. DR InterPro; IPR000595; cNMP-bd_dom. DR InterPro; IPR018490; cNMP-bd_dom_sf. DR InterPro; IPR012318; HTH_CRP. DR InterPro; IPR014710; RmlC-like_jellyroll. DR InterPro; IPR018335; Tscrpt_reg_HTH_Crp-type_CS. DR InterPro; IPR036388; WH-like_DNA-bd_sf. DR InterPro; IPR036390; WH_DNA-bd_sf. DR Pfam; PF00027; cNMP_binding; 1. DR Pfam; PF00325; Crp; 1. DR PRINTS; PR00034; HTHCRP. DR SMART; SM00100; cNMP; 1. DR SMART; SM00419; HTH_CRP; 1. DR SUPFAM; SSF51206; cAMP-binding domain-like; 1. DR SUPFAM; SSF46785; Winged helix DNA-binding domain; 1. DR PROSITE; PS50042; CNMP_BINDING_3; 1. DR PROSITE; PS00042; HTH_CRP_1; 1. DR PROSITE; PS51063; HTH_CRP_2; 1. PE 1: Evidence at protein level; KW 4Fe-4S; Activator; Cytoplasm; Direct protein sequencing; DNA-binding; Iron; KW Iron-sulfur; Metal-binding; Reference proteome; Repressor; Transcription; KW Transcription regulation. FT CHAIN 1..250 FT /note="Fumarate and nitrate reduction regulatory protein" FT /id="PRO_0000100161" FT DOMAIN 164..237 FT /note="HTH crp-type" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00387" FT DNA_BIND 197..216 FT /note="H-T-H motif" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00387" FT REGION 20..29 FT /note="Essential for the oxygen-regulated activity" FT REGION 47..50 FT /note="Activating region 2A" FT /evidence="ECO:0000255" FT REGION 60..61 FT /note="Activating region 3A" FT /evidence="ECO:0000255" FT REGION 71..75 FT /note="Activating region 1A" FT /evidence="ECO:0000255" FT REGION 81 FT /note="Activating region 3B" FT /evidence="ECO:0000255" FT REGION 85..87 FT /note="Activating region 3C" FT /evidence="ECO:0000255" FT REGION 112 FT /note="Activating region 3D" FT /evidence="ECO:0000255" FT REGION 116..121 FT /note="Activating region 1B" FT /evidence="ECO:0000255" FT REGION 123..124 FT /note="Activating region 2B" FT /evidence="ECO:0000255" FT REGION 127..128 FT /note="Activating region 2C" FT /evidence="ECO:0000255" FT REGION 140..159 FT /note="Dimerization" FT /evidence="ECO:0000255" FT REGION 181..191 FT /note="Activating region 1C" FT /evidence="ECO:0000255" FT BINDING 20 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /evidence="ECO:0000255" FT BINDING 23 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /evidence="ECO:0000255" FT BINDING 29 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /evidence="ECO:0000255" FT BINDING 122 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /evidence="ECO:0000255" FT MUTAGEN 16 FT /note="C->A: No effect." FT /evidence="ECO:0000269|PubMed:2226775" FT MUTAGEN 20 FT /note="C->S: Loss of activity." FT /evidence="ECO:0000269|PubMed:2226775" FT MUTAGEN 22 FT /note="D->G: Loss of regulation by O(2)." FT /evidence="ECO:0000269|PubMed:1898918" FT MUTAGEN 23 FT /note="C->G: Loss of activity." FT /evidence="ECO:0000269|PubMed:2226775" FT MUTAGEN 28 FT /note="L->H: Loss of regulation by O(2)." FT /evidence="ECO:0000269|PubMed:1898918" FT MUTAGEN 29 FT /note="C->G: Loss of activity." FT /evidence="ECO:0000269|PubMed:2226775" FT MUTAGEN 43 FT /note="D->G: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:9321653" FT MUTAGEN 64 FT /note="E->Q: No effect." FT /evidence="ECO:0000269|PubMed:2226775" FT MUTAGEN 72 FT /note="R->H: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:9321653" FT MUTAGEN 73 FT /note="S->F: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:11115116, FT ECO:0000269|PubMed:9321653" FT MUTAGEN 81 FT /note="I->T: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:1762901" FT MUTAGEN 82 FT /note="T->P: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:1762901" FT MUTAGEN 85 FT /note="G->A: Decrease in activity; no effect on DNA- FT binding. Trace activity; when associated with P-187." FT /evidence="ECO:0000269|PubMed:11115116, FT ECO:0000269|PubMed:1762901" FT MUTAGEN 86 FT /note="D->A: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:1762901" FT MUTAGEN 87 FT /note="E->K: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:1762901" FT MUTAGEN 88 FT /note="Q->E: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:1762901" FT MUTAGEN 93 FT /note="H->R: Loss of regulation by O(2)." FT /evidence="ECO:0000269|PubMed:1898918" FT MUTAGEN 96 FT /note="G->D: Loss of activity." FT /evidence="ECO:0000269|PubMed:2226775" FT MUTAGEN 118 FT /note="T->A,P: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:11115116, FT ECO:0000269|PubMed:9321653" FT MUTAGEN 120 FT /note="M->I,R,T,V: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:9321653" FT MUTAGEN 122 FT /note="C->A,S: Loss of activity." FT /evidence="ECO:0000269|PubMed:2226775" FT MUTAGEN 140 FT /note="R->A: Decrease in activity." FT MUTAGEN 143 FT /note="M->A: Decrease in activity." FT MUTAGEN 144 FT /note="M->A: Decrease in activity due to faulty FT dimerization." FT MUTAGEN 145 FT /note="R->A: Decrease in activity." FT MUTAGEN 146 FT /note="L->A: Decrease in activity." FT MUTAGEN 147 FT /note="M->A: Decrease in activity due to faulty FT dimerization." FT MUTAGEN 150 FT /note="E->K: Loss of regulation by O(2)." FT /evidence="ECO:0000269|PubMed:1898918" FT MUTAGEN 151 FT /note="I->A: Decrease in activity due to faulty FT dimerization." FT MUTAGEN 154 FT /note="D->A,G,V: Loss of regulation by O(2)." FT /evidence="ECO:0000269|PubMed:1898918, FT ECO:0000269|PubMed:8406003" FT MUTAGEN 158 FT /note="I->A: Decrease in activity due to faulty FT dimerization." FT MUTAGEN 181 FT /note="F->L: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:9321653" FT MUTAGEN 186 FT /note="F->S: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:9321653" FT MUTAGEN 187 FT /note="S->P: Decrease in activity; no effect on DNA- FT binding. Trace activity; when associated with A-85." FT /evidence="ECO:0000269|PubMed:11115116, FT ECO:0000269|PubMed:9321653" FT MUTAGEN 191 FT /note="F->L: Decrease in activity; no effect on DNA- FT binding." FT /evidence="ECO:0000269|PubMed:9321653" SQ SEQUENCE 250 AA; 27967 MW; 33F7BFA2972FF703 CRC64; MIPEKRIIRR IQSGGCAIHC QDCSISQLCI PFTLNEHELD QLDNIIERKK PIQKGQTLFK AGDELKSLYA IRSGTIKSYT ITEQGDEQIT GFHLAGDLVG FDAIGSGHHP SFAQALETSM VCEIPFETLD DLSGKMPNLR QQMMRLMSGE IKGDQDMILL LSKKNAEERL AAFIYNLSRR FAQRGFSPRE FRLTMTRGDI GNYLGLTVET ISRLLGRFQK SGMLAVKGKY ITIENNDALA QLAGHTRNVA //