RFAH_ECOLI
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 03-AUG-2022, entry version 123.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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}.
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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_STEB01000021.1.
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 PDBsum; 2OUG; -.
DR PDBsum; 5OND; -.
DR PDBsum; 6C6S; -.
DR PDBsum; 6C6T; -.
DR AlphaFoldDB; P0AFW0; -.
DR BMRB; P0AFW0; -.
DR SMR; P0AFW0; -.
DR IntAct; P0AFW0; 7.
DR STRING; 511145.b3842; -.
DR MoonProt; P0AFW0; -.
DR jPOST; P0AFW0; -.
DR PaxDb; P0AFW0; -.
DR PRIDE; P0AFW0; -.
DR EnsemblBacteria; AAC76845; AAC76845; b3842.
DR EnsemblBacteria; BAE77461; BAE77461; BAE77461.
DR GeneID; 66672252; -.
DR GeneID; 948327; -.
DR KEGG; ecj:JW3818; -.
DR KEGG; eco:b3842; -.
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; NQGVECF; -.
DR PhylomeDB; P0AFW0; -.
DR BioCyc; EcoCyc:EG10839-MON; -.
DR EvolutionaryTrace; P0AFW0; -.
DR PRO; PR:P0AFW0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
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 Gene3D; 3.30.70.940; -; 1.
DR HAMAP; MF_00951; RfaH; 1.
DR InterPro; IPR006645; NGN_dom.
DR InterPro; IPR036735; NGN_dom_sf.
DR InterPro; IPR043425; NusG-like.
DR InterPro; IPR010215; Transcription_antiterm_RfaH.
DR PANTHER; PTHR30265; PTHR30265; 1.
DR Pfam; PF02357; NusG; 1.
DR SMART; SM00738; NGN; 1.
DR SUPFAM; SSF82679; SSF82679; 1.
DR TIGRFAMs; TIGR01955; RfaH; 1.
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 75..78
FT /evidence="ECO:0007829|PDB:2OUG"
FT STRAND 81..85
FT /evidence="ECO:0007829|PDB:2OUG"
FT HELIX 91..98
FT /evidence="ECO:0007829|PDB:2OUG"
FT HELIX 118..129
FT /evidence="ECO:0007829|PDB:2OUG"
FT HELIX 135..155
FT /evidence="ECO:0007829|PDB:2OUG"
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
