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 01-MAY-2013, entry version 69. 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; Enterobacteriales; 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., RA Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., RA Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., RA Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., RA Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.; RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome RT corresponding to 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., RA Mau B., Shao Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1474(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 RT MG1655 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., RA Guest J.R., 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; RA Lazazzera B.A., Bates D.M., Kiley P.J.; RT "The activity of the Escherichia coli transcription factor FNR is RT regulated 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 RT coli by O2: [4Fe-4S] to [2Fe-2S] conversion with loss of biological RT 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 RP 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; RA Kiley P.J., Reznikoff W.S.; RT "Fnr mutants that activate gene expression in the presence of RT 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 RT the 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; RP PHE-181; 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=10.1016/S0168-6445(05)80007-5; 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=10.1016/S0168-6445(98)00022-9; RA Kiley P.J., Beinert H.; RT "Oxygen sensing by the global regulator, FNR: the role of the iron- RT sulfur 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 CC of over 100 target genes in response to anoxia. It facilitates the CC adaptation to anaerobic growth conditions by regulating the CC expression of gene products that are involved in anaerobic energy CC metabolism. When the terminal electron acceptor, O(2), is no CC longer available, it represses the synthesis of enzymes involved CC in aerobic respiration and increases the synthesis of enzymes CC required for anaerobic respiration. CC -!- COFACTOR: Binds 1 4Fe-4S cluster per subunit. CC -!- SUBUNIT: Homodimer. CC -!- SUBCELLULAR LOCATION: Cytoplasm (Probable). CC -!- DOMAIN: The amino acid residues contacting the FNR target site on CC the DNA (5'-TTGATNNNNATCAA-3') are located in the putative DNA- CC recognition helix (alphaF), which contains the FNR motif (EXXSR). CC Three surface-exposed loops forming activating region 1 (AR1) in CC the downstream subunit of the dimer contact the C-terminal domain CC of the alpha subunit (alphaCTD) of RNA polymerase for activation CC of class I promoters (the 161-121 loop is the major AR1 activating CC determinant). At class II promoters, the AR1 of the upstream CC subunit contacts alphaCTD, promoting open complex formation; CC activating region 3 (AR3) of the downstream subunit contacts CC region 4 of the sigma70 subunit of RNA polymerase, to effect CC direct activation. At promoters repressed by FNR, tandem FNR CC dimers might interact with each other at AR1 to restrict access to CC a 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 Range=10-250; Source=PubMed:8497198; CC -!- MISCELLANEOUS: FNR senses the oxygen concentration directly via CC the disassembly and reassembly of the [4Fe-4S] clusters. CC Anaerobic, de novo acquisition of the iron-sulfur cluster converts CC monomeric, inactive apo-FNR into a dimeric form containing two CC [4Fe-4S] clusters. This, in turn, enhances the affinity of FNR for CC specific DNA targets and mediates transcription regulation by CC establishing direct FNR-RNA polymerase contacts. With the increase CC in intracellular oxygen concentration, the [4Fe-4S] cluster is CC oxidized, producing a [2Fe-2S] cluster, which decays to apo-FNR. CC Apo-FNR [4SH] can be reversibly oxidized to a disulfide form CC [2SH,S-S], suggesting that FNR may be able to sense oxidative CC stress as well as normoxia. This interconversion may be mediated CC by agents such as glutathione or thioredoxin. CC -!- SIMILARITY: Contains 1 cyclic nucleotide-binding domain. CC -!- SIMILARITY: Contains 1 HTH crp-type DNA-binding domain. 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_000913.2. DR RefSeq; YP_489604.1; NC_007779.1. DR ProteinModelPortal; P0A9E5; -. DR SMR; P0A9E5; 47-241. DR IntAct; P0A9E5; 6. DR MINT; MINT-1237977; -. DR STRING; 511145.b1334; -. DR PaxDb; P0A9E5; -. DR PRIDE; P0A9E5; -. DR EnsemblBacteria; AAC74416; AAC74416; b1334. DR EnsemblBacteria; BAA14927; BAA14927; BAA14927. DR GeneID; 12932858; -. DR GeneID; 945908; -. DR KEGG; ecj:Y75_p1311; -. DR KEGG; eco:b1334; -. DR PATRIC; 32117944; VBIEscCol129921_1392. DR EchoBASE; EB0321; -. DR EcoGene; EG10325; fnr. DR eggNOG; COG0664; -. DR HOGENOM; HOG000186461; -. DR KO; K01420; -. DR OMA; FSANQFR; -. DR ProtClustDB; PRK11161; -. DR BioCyc; EcoCyc:PD00197; -. DR BioCyc; ECOL316407:JW1328-MONOMER; -. DR Genevestigator; P0A9E5; -. DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell. 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:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0003700; F:sequence-specific DNA binding transcription factor activity; IDA:EcoCyc. DR GO; GO:0009061; P:anaerobic respiration; IEP:EcoCyc. DR GO; GO:0071731; P:response to nitric oxide; IEP:EcoCyc. DR GO; GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. DR Gene3D; 1.10.10.10; -; 1. DR Gene3D; 2.60.120.10; -; 1. DR InterPro; IPR018490; cNMP-bd-like. DR InterPro; IPR000595; cNMP-bd_dom. DR InterPro; IPR012318; HTH_CRP_2. DR InterPro; IPR014710; RmlC-like_jellyroll. DR InterPro; IPR001808; Tscrpt_reg_HTH_Crp. DR InterPro; IPR018335; Tscrpt_reg_HTH_Crp-type_CS. DR InterPro; IPR011991; WHTH_DNA-bd_dom. 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; cNMP_binding; 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; Complete proteome; Cytoplasm; KW Direct protein sequencing; DNA-binding; Iron; Iron-sulfur; KW Metal-binding; Reference proteome; Repressor; Transcription; KW Transcription regulation. FT CHAIN 1 250 Fumarate and nitrate reduction regulatory FT protein. FT /FTId=PRO_0000100161. FT DOMAIN 164 237 HTH crp-type. FT DNA_BIND 197 216 H-T-H motif (By similarity). FT REGION 20 29 Essential for the oxygen-regulated FT activity. FT REGION 47 50 Activating region 2A (Potential). FT REGION 60 61 Activating region 3A (Potential). FT REGION 71 75 Activating region 1A (Potential). FT REGION 81 81 Activating region 3B (Potential). FT REGION 85 87 Activating region 3C (Potential). FT REGION 112 112 Activating region 3D (Potential). FT REGION 116 121 Activating region 1B (Potential). FT REGION 123 124 Activating region 2B (Potential). FT REGION 127 128 Activating region 2C (Potential). FT REGION 140 159 Dimerization (Potential). FT REGION 181 191 Activating region 1C (Potential). FT METAL 20 20 Iron-sulfur (4Fe-4S) (Potential). FT METAL 23 23 Iron-sulfur (4Fe-4S) (Potential). FT METAL 29 29 Iron-sulfur (4Fe-4S) (Potential). FT METAL 122 122 Iron-sulfur (4Fe-4S) (Potential). FT MUTAGEN 16 16 C->A: No effect. FT MUTAGEN 20 20 C->S: Loss of activity. FT MUTAGEN 22 22 D->G: Loss of regulation by O(2). FT MUTAGEN 23 23 C->G: Loss of activity. FT MUTAGEN 28 28 L->H: Loss of regulation by O(2). FT MUTAGEN 29 29 C->G: Loss of activity. FT MUTAGEN 43 43 D->G: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 64 64 E->Q: No effect. FT MUTAGEN 72 72 R->H: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 73 73 S->F: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 81 81 I->T: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 82 82 T->P: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 85 85 G->A: Decrease in activity; no effect on FT DNA-binding. Trace activity; when FT associated with P-187. FT MUTAGEN 86 86 D->A: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 87 87 E->K: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 88 88 Q->E: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 93 93 H->R: Loss of regulation by O(2). FT MUTAGEN 96 96 G->D: Loss of activity. FT MUTAGEN 118 118 T->A,P: Decrease in activity; no effect FT on DNA-binding. FT MUTAGEN 120 120 M->I,R,T,V: Decrease in activity; no FT effect on DNA-binding. FT MUTAGEN 122 122 C->A,S: Loss of activity. FT MUTAGEN 140 140 R->A: Decrease in activity. FT MUTAGEN 143 143 M->A: Decrease in activity. FT MUTAGEN 144 144 M->A: Decrease in activity due to faulty FT dimerization. FT MUTAGEN 145 145 R->A: Decrease in activity. FT MUTAGEN 146 146 L->A: Decrease in activity. FT MUTAGEN 147 147 M->A: Decrease in activity due to faulty FT dimerization. FT MUTAGEN 150 150 E->K: Loss of regulation by O(2). FT MUTAGEN 151 151 I->A: Decrease in activity due to faulty FT dimerization. FT MUTAGEN 154 154 D->A,G,V: Loss of regulation by O(2). FT MUTAGEN 158 158 I->A: Decrease in activity due to faulty FT dimerization. FT MUTAGEN 181 181 F->L: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 186 186 F->S: Decrease in activity; no effect on FT DNA-binding. FT MUTAGEN 187 187 S->P: Decrease in activity; no effect on FT DNA-binding. Trace activity; when FT associated with A-85. FT MUTAGEN 191 191 F->L: Decrease in activity; no effect on FT DNA-binding. 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 //