ID RFAH_ECOLI Reviewed; 162 AA. AC P0AFW0; P26614; Q2M8E5; DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot. DT 20-DEC-2005, sequence version 1. DT 10-JUN-2026, entry version 140. DE RecName: Full=Transcription antitermination protein RfaH {ECO:0000255|HAMAP-Rule:MF_00951}; GN Name=rfaH {ECO:0000255|HAMAP-Rule:MF_00951}; Synonyms=hlyT, sfrB; GN OrderedLocusNames=b3842, JW3818; OS Escherichia coli (strain K12). OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; OC Enterobacterales; Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION. RC STRAIN=5KC; RX PubMed=1584020; DOI=10.1111/j.1365-2958.1992.tb02166.x; RA Bailey M.J.A., Koronakis V., Schmoll T., Hughes C.; RT "Escherichia coli HlyT protein, a transcriptional activator of haemolysin RT synthesis and secretion, is encoded by the rfaH (sfrB) locus required for RT expression of sex factor and lipopolysaccharide genes."; RL Mol. Microbiol. 6:1003-1012(1992). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=K12; RA Missiakas D., Georgopoulos C., Raina S.; RL Submitted (MAR-1996) to the EMBL/GenBank/DDBJ databases. RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=1379743; DOI=10.1126/science.1379743; RA Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.; RT "Analysis of the Escherichia coli genome: DNA sequence of the region from RT 84.5 to 86.5 minutes."; RL Science 257:771-778(1992). RN [4] 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 [5] 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 [6] RP FUNCTION IN HEMOLYSIN TRANSCRIPTION. RC STRAIN=5KC; RX PubMed=8606157; DOI=10.1128/jb.178.7.1850-1857.1996; RA Leeds J.A., Welch R.A.; RT "RfaH enhances elongation of Escherichia coli hlyCABD mRNA."; RL J. Bacteriol. 178:1850-1857(1996). RN [7] RP FUNCTION. RX PubMed=8951819; DOI=10.1046/j.1365-2958.1996.d01-1726.x; RA Bailey M.J., Hughes C., Koronakis V.; RT "Increased distal gene transcription by the elongation factor RfaH, a RT specialized homologue of NusG."; RL Mol. Microbiol. 22:729-737(1996). RN [8] RP FUNCTION. RX PubMed=9171395; DOI=10.1128/jb.179.11.3519-3527.1997; RA Leeds J.A., Welch R.A.; RT "Enhancing transcription through the Escherichia coli hemolysin operon, RT hlyCABD: RfaH and upstream JUMPStart DNA sequences function together via a RT postinitiation mechanism."; RL J. Bacteriol. 179:3519-3527(1997). RN [9] RP FUNCTION. RX PubMed=9426123; DOI=10.1046/j.1365-2958.1997.6432014.x; RA Bailey M.J., Hughes C., Koronakis V.; RT "RfaH and the ops element, components of a novel system controlling RT bacterial transcription elongation."; RL Mol. Microbiol. 26:845-851(1997). RN [10] RP FUNCTION. RX PubMed=10660066; DOI=10.1007/pl00008648; RA Bailey M.J., Hughes C., Koronakis V.; RT "In vitro recruitment of the RfaH regulatory protein into a specialised RT transcription complex, directed by the nucleic acid ops element."; RL Mol. Gen. Genet. 262:1052-1059(2000). RN [11] RP FUNCTION, AND INTERACTION WITH DNA AND RNAP. RX PubMed=12007406; DOI=10.1016/s0092-8674(02)00724-9; RA Artsimovitch I., Landick R.; RT "The transcriptional regulator RfaH stimulates RNA chain synthesis after RT recruitment to elongation complexes by the exposed nontemplate DNA RT strand."; RL Cell 109:193-203(2002). RN [12] RP FUNCTION. RX PubMed=11983161; DOI=10.1016/s1097-2765(02)00516-6; RA Santangelo T.J., Roberts J.W.; RT "RfaH, a bacterial transcription antiterminator."; RL Mol. Cell 9:698-700(2002). RN [13] RP FUNCTION IN BIOFILM FORMATION, AND DISRUPTION PHENOTYPE. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=16452414; DOI=10.1128/jb.188.4.1316-1331.2006; RA Beloin C., Michaelis K., Lindner K., Landini P., Hacker J., Ghigo J.M., RA Dobrindt U.; RT "The transcriptional antiterminator RfaH represses biofilm formation in RT Escherichia coli."; RL J. Bacteriol. 188:1316-1331(2006). RN [14] RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), SUBUNIT, AND DOMAIN. RX PubMed=17434131; DOI=10.1016/j.molcel.2007.02.021; RA Belogurov G.A., Vassylyeva M.N., Svetlov V., Klyuyev S., Grishin N.V., RA Vassylyev D.G., Artsimovitch I.; RT "Structural basis for converting a general transcription factor into an RT operon-specific virulence regulator."; RL Mol. Cell 26:117-129(2007). CC -!- FUNCTION: Enhances distal genes transcription elongation in a CC specialized subset of operons that encode extracytoplasmic components. CC RfaH is recruited into a multi-component RNA polymerase complex by the CC ops element, which is a short conserved DNA sequence located downstream CC of the main promoter of these operons. Once bound, RfaH suppresses CC pausing and inhibits Rho-dependent and intrinsic termination at a CC subset of sites. Termination signals are bypassed, which allows CC complete synthesis of long RNA chains. Enhances expression of several CC operons involved in synthesis of lipopolysaccharides, CC exopolysaccharides, hemolysin, and sex factor. Also negatively controls CC expression and surface presentation of AG43 and possibly another AG43- CC independent factor that mediates cell-cell interactions and biofilm CC formation. {ECO:0000255|HAMAP-Rule:MF_00951, CC ECO:0000269|PubMed:10660066, ECO:0000269|PubMed:11983161, CC ECO:0000269|PubMed:12007406, ECO:0000269|PubMed:1584020, CC ECO:0000269|PubMed:16452414, ECO:0000269|PubMed:8606157, CC ECO:0000269|PubMed:8951819, ECO:0000269|PubMed:9171395, CC ECO:0000269|PubMed:9426123}. CC -!- SUBUNIT: Interacts with both the nontemplate DNA and the RNA polymerase CC (RNAP). Monomer in solution. {ECO:0000255|HAMAP-Rule:MF_00951, CC ECO:0000269|PubMed:12007406, ECO:0000269|PubMed:17434131}. CC -!- DOMAIN: The N-terminal domain contains a vast hydrophobic cavity that CC is buried by the C-terminal domain. This cavity may bind the RNAP and CC become unmasked only upon binding to the nontemplate DNA strand. CC {ECO:0000269|PubMed:17434131}. CC -!- DISRUPTION PHENOTYPE: Inactivation results in increased initial CC adhesion and biofilm formation. {ECO:0000269|PubMed:16452414}. CC -!- SIMILARITY: Belongs to the RfaH family. {ECO:0000255|HAMAP- CC Rule:MF_00951}. 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; X65013; CAA46147.1; -; Genomic_DNA. DR EMBL; M87049; AAA67638.1; -; Genomic_DNA. DR EMBL; M94889; AAA91060.1; -; Genomic_DNA. DR EMBL; U00096; AAC76845.1; -; Genomic_DNA. DR EMBL; AP009048; BAE77461.1; -; Genomic_DNA. DR PIR; S30732; S30732. DR RefSeq; NP_418284.1; NC_000913.3. DR RefSeq; WP_001192396.1; NZ_CP009789.1. DR PDB; 2LCL; NMR; -; A=101-162. DR PDB; 2OUG; X-ray; 2.10 A; A/B/C/D=1-162. DR PDB; 5OND; X-ray; 2.10 A; A/B=1-162. DR PDB; 6C6S; EM; 3.70 A; D=1-162. DR PDB; 6C6T; EM; 3.50 A; D=1-162. DR PDB; 8PEN; EM; 3.10 A; P=1-162. DR PDB; 8PFG; EM; 3.10 A; P=1-162. DR PDB; 8PFJ; EM; 3.40 A; P=1-162. DR PDB; 8PHK; EM; 3.10 A; P=1-162. DR PDB; 8PIB; EM; 2.60 A; P=1-162. DR PDB; 8PID; EM; 3.00 A; P=1-162. DR PDB; 8PIL; EM; 3.20 A; P=1-162. DR PDB; 8PIM; EM; 3.40 A; P=1-162. DR PDB; 8UPO; EM; 5.50 A; AB=1-162. DR PDB; 8UPR; EM; 5.30 A; AB=1-162. DR PDB; 8UQL; EM; 3.20 A; AB=1-162. DR PDB; 8UQM; EM; 5.30 A; AB=1-162. DR PDB; 8UQP; EM; 3.80 A; AB=1-162. DR PDB; 8UR0; EM; 3.40 A; AB=1-162. DR PDB; 8URH; EM; 5.70 A; AB=1-162. DR PDB; 8URI; EM; 5.30 A; AB=1-162. DR PDB; 8URX; EM; 6.60 A; AB=1-162. DR PDB; 8URY; EM; 3.10 A; AB=1-162. DR AlphaFoldDB; P0AFW0; -. DR BMRB; P0AFW0; -. DR EMDB; EMD-17632; -. DR EMDB; EMD-17646; -. DR EMDB; EMD-17647; -. DR EMDB; EMD-17668; -. DR EMDB; EMD-17679; -. DR EMDB; EMD-17681; -. DR EMDB; EMD-17685; -. DR EMDB; EMD-17686; -. DR EMDB; EMD-7349; -. DR EMDB; EMD-7350; -. DR SMR; P0AFW0; -. DR BioGRID; 4263465; 8. DR FunCoup; P0AFW0; 31. DR IntAct; P0AFW0; 7. DR STRING; 511145.b3842; -. DR MoonProt; P0AFW0; -. DR jPOST; P0AFW0; -. DR PaxDb; 511145-b3842; -. DR EnsemblBacteria; AAC76845; AAC76845; b3842. DR GeneID; 86948508; -. DR GeneID; 948327; -. DR KEGG; ecj:JW3818; -. DR KEGG; eco:b3842; -. DR KEGG; ecoc:C3026_20775; -. DR PATRIC; fig|1411691.4.peg.2868; -. DR EchoBASE; EB0832; -. DR eggNOG; COG0250; Bacteria. DR HOGENOM; CLU_067287_5_0_6; -. DR InParanoid; P0AFW0; -. DR OMA; AVYVRSR; -. DR OrthoDB; 9790639at2; -. DR PhylomeDB; P0AFW0; -. DR BioCyc; EcoCyc:EG10839-MONOMER; -. DR EvolutionaryTrace; P0AFW0; -. DR PRO; PR:P0AFW0; -. DR Proteomes; UP000000625; Chromosome. DR GO; GO:0005829; C:cytosol; IBA:GO_Central. DR GO; GO:0001000; F:bacterial-type RNA polymerase core enzyme binding; IDA:EcoCyc. DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule. DR GO; GO:0061980; F:regulatory RNA binding; IDA:EcoCyc. DR GO; GO:0001073; F:transcription antitermination factor activity, DNA binding; IDA:EcoCyc. DR GO; GO:0008494; F:translation activator activity; IMP:EcoCyc. DR GO; GO:0006354; P:DNA-templated transcription elongation; IDA:EcoCyc. DR GO; GO:0045727; P:positive regulation of translation; IMP:EcoCyc. DR GO; GO:0031564; P:transcription antitermination; IDA:EcoCyc. DR CDD; cd09892; NGN_SP_RfaH; 1. DR DisProt; DP03913; -. DR FunFam; 3.30.70.940:FF:000004; Transcription antitermination protein RfaH; 1. DR Gene3D; 3.30.70.940; NusG, N-terminal domain; 1. DR HAMAP; MF_00951; RfaH; 1. DR InterPro; IPR006645; NGN-like_dom. DR InterPro; IPR036735; NGN_dom_sf. DR InterPro; IPR043425; NusG-like. DR InterPro; IPR010215; Transcription_antiterm_RfaH. DR NCBIfam; NF006534; PRK09014.1; 1. DR NCBIfam; TIGR01955; RfaH; 1. DR PANTHER; PTHR30265; RHO-INTERACTING TRANSCRIPTION TERMINATION FACTOR NUSG; 1. DR PANTHER; PTHR30265:SF7; TRANSCRIPTION ANTITERMINATION PROTEIN RFAH; 1. DR Pfam; PF02357; NusG; 1. DR SMART; SM00738; NGN; 1. DR SUPFAM; SSF82679; N-utilization substance G protein NusG, N-terminal domain; 1. DR PDBsum; 2LCL; -. DR PDBsum; 2OUG; -. DR PDBsum; 5OND; -. DR PDBsum; 6C6S; -. DR PDBsum; 6C6T; -. DR PDBsum; 8PEN; -. DR PDBsum; 8PFG; -. DR PDBsum; 8PFJ; -. DR PDBsum; 8PHK; -. DR PDBsum; 8PIB; -. DR PDBsum; 8PID; -. DR PDBsum; 8PIL; -. DR PDBsum; 8PIM; -. DR PDBsum; 8UPO; -. DR PDBsum; 8UPR; -. DR PDBsum; 8UQL; -. DR PDBsum; 8UQM; -. DR PDBsum; 8UQP; -. DR PDBsum; 8UR0; -. DR PDBsum; 8URH; -. DR PDBsum; 8URI; -. DR PDBsum; 8URX; -. DR PDBsum; 8URY; -. PE 1: Evidence at protein level; KW 3D-structure; DNA-binding; Reference proteome; Transcription; KW Transcription antitermination; Transcription regulation. FT CHAIN 1..162 FT /note="Transcription antitermination protein RfaH" FT /id="PRO_0000097281" FT STRAND 3..9 FT /evidence="ECO:0007829|PDB:2OUG" FT TURN 11..13 FT /evidence="ECO:0007829|PDB:2OUG" FT HELIX 14..23 FT /evidence="ECO:0007829|PDB:2OUG" FT STRAND 27..29 FT /evidence="ECO:0007829|PDB:2OUG" FT STRAND 32..51 FT /evidence="ECO:0007829|PDB:2OUG" FT STRAND 54..59 FT /evidence="ECO:0007829|PDB:2OUG" FT TURN 61..63 FT /evidence="ECO:0007829|PDB:2OUG" FT HELIX 66..71 FT /evidence="ECO:0007829|PDB:2OUG" FT STRAND 72..74 FT /evidence="ECO:0007829|PDB:8URY" FT STRAND 75..78 FT /evidence="ECO:0007829|PDB:2OUG" FT STRAND 81..85 FT /evidence="ECO:0007829|PDB:2OUG" FT HELIX 86..89 FT /evidence="ECO:0007829|PDB:8URY" FT HELIX 91..98 FT /evidence="ECO:0007829|PDB:2OUG" FT STRAND 102..105 FT /evidence="ECO:0007829|PDB:2LCL" FT STRAND 106..108 FT /evidence="ECO:0007829|PDB:8PHK" FT STRAND 114..117 FT /evidence="ECO:0007829|PDB:8UQL" FT HELIX 118..129 FT /evidence="ECO:0007829|PDB:2OUG" FT HELIX 135..155 FT /evidence="ECO:0007829|PDB:2OUG" FT TURN 156..158 FT /evidence="ECO:0007829|PDB:8PID" FT STRAND 159..161 FT /evidence="ECO:0007829|PDB:8PID" SQ SEQUENCE 162 AA; 18340 MW; 2A298947EBB58C65 CRC64; MQSWYLLYCK RGQLQRAQEH LERQAVNCLA PMITLEKIVR GKRTAVSEPL FPNYLFVEFD PEVIHTTTIN ATRGVSHFVR FGASPAIVPS AVIHQLSVYK PKDIVDPATP YPGDKVIITE GAFEGFQAIF TEPDGEARSM LLLNLINKEI KHSVKNTEFR KL //