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Protein

Transcription antitermination protein RfaH

Gene

rfaH

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Enhances distal genes transcription elongation in a specialized subset of operons that encode extracytoplasmic components. RfaH is recruited into a multi-component RNA polymerase complex by the ops element, which is a short conserved DNA sequence located downstream of the main promoter of these operons. Once bound, RfaH suppresses pausing and inhibits Rho-dependent and intrinsic termination at a subset of sites. Termination signals are bypassed, which allows complete synthesis of long RNA chains. Enhances expression of several operons involved in synthesis of lipopolysaccharides, exopolysaccharides, hemolysin, and sex factor. Also negatively controls expression and surface presentation of AG43 and possibly another AG43-independent factor that mediates cell-cell interactions and biofilm formation.UniRule annotation9 Publications

GO - Molecular functioni

  • bacterial-type RNA polymerase core enzyme binding Source: EcoCyc
  • DNA binding Source: UniProtKB-HAMAP
  • transcription antitermination factor activity, DNA binding Source: EcoCyc
  • translation activator activity Source: EcoCyc

GO - Biological processi

  • positive regulation of translation Source: EcoCyc
  • transcription antitermination Source: EcoCyc
  • transcription elongation from bacterial-type RNA polymerase promoter Source: EcoCyc
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription antitermination, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10839-MONOMER.
ECOL316407:JW3818-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription antitermination protein RfaHUniRule annotation
Gene namesi
Name:rfaHUniRule annotation
Synonyms:hlyT, sfrB
Ordered Locus Names:b3842, JW3818
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10839. rfaH.

Pathology & Biotechi

Disruption phenotypei

Inactivation results in increased initial adhesion and biofilm formation.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 162162Transcription antitermination protein RfaHPRO_0000097281Add
BLAST

Proteomic databases

PaxDbiP0AFW0.
PRIDEiP0AFW0.

Interactioni

Subunit structurei

Interacts with both the nontemplate DNA and the RNA polymerase (RNAP). Monomer in solution.UniRule annotation2 Publications

GO - Molecular functioni

  • bacterial-type RNA polymerase core enzyme binding Source: EcoCyc

Protein-protein interaction databases

IntActiP0AFW0. 7 interactions.
STRINGi511145.b3842.

Structurei

Secondary structure

1
162
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97Combined sources
Turni11 – 133Combined sources
Helixi14 – 2310Combined sources
Beta strandi27 – 293Combined sources
Beta strandi32 – 5120Combined sources
Beta strandi54 – 596Combined sources
Turni61 – 633Combined sources
Helixi66 – 716Combined sources
Beta strandi75 – 784Combined sources
Beta strandi81 – 855Combined sources
Helixi91 – 988Combined sources
Helixi118 – 12912Combined sources
Helixi135 – 15521Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2OUGX-ray2.10A/B/C/D1-162[»]
ProteinModelPortaliP0AFW0.
SMRiP0AFW0. Positions 2-162.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AFW0.

Family & Domainsi

Domaini

The N-terminal domain contains a vast hydrophobic cavity that is buried by the C-terminal domain. This cavity may bind the RNAP and become unmasked only upon binding to the nontemplate DNA strand.1 Publication

Sequence similaritiesi

Belongs to the RfaH family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105MDZ. Bacteria.
COG0250. LUCA.
HOGENOMiHOG000272711.
InParanoidiP0AFW0.
KOiK05785.
OMAiNCLTPMI.
OrthoDBiEOG6KHG0C.

Family and domain databases

Gene3Di3.30.70.940. 1 hit.
HAMAPiMF_00951. RfaH.
InterProiIPR006645. NGN_dom.
IPR010215. Transcription_antiterm_RfaH.
[Graphical view]
PfamiPF02357. NusG. 1 hit.
[Graphical view]
SMARTiSM00738. NGN. 1 hit.
[Graphical view]
SUPFAMiSSF82679. SSF82679. 1 hit.
TIGRFAMsiTIGR01955. RfaH. 1 hit.

Sequencei

Sequence statusi: Complete.

P0AFW0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQSWYLLYCK RGQLQRAQEH LERQAVNCLA PMITLEKIVR GKRTAVSEPL
60 70 80 90 100
FPNYLFVEFD PEVIHTTTIN ATRGVSHFVR FGASPAIVPS AVIHQLSVYK
110 120 130 140 150
PKDIVDPATP YPGDKVIITE GAFEGFQAIF TEPDGEARSM LLLNLINKEI
160
KHSVKNTEFR KL
Length:162
Mass (Da):18,340
Last modified:December 20, 2005 - v1
Checksum:i2A298947EBB58C65
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X65013 Genomic DNA. Translation: CAA46147.1.
M87049 Genomic DNA. Translation: AAA67638.1.
M94889 Genomic DNA. Translation: AAA91060.1.
U00096 Genomic DNA. Translation: AAC76845.1.
AP009048 Genomic DNA. Translation: BAE77461.1.
PIRiS30732.
RefSeqiNP_418284.1. NC_000913.3.
WP_001192396.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76845; AAC76845; b3842.
BAE77461; BAE77461; BAE77461.
GeneIDi948327.
KEGGiecj:JW3818.
eco:b3842.
PATRICi32123181. VBIEscCol129921_3956.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X65013 Genomic DNA. Translation: CAA46147.1.
M87049 Genomic DNA. Translation: AAA67638.1.
M94889 Genomic DNA. Translation: AAA91060.1.
U00096 Genomic DNA. Translation: AAC76845.1.
AP009048 Genomic DNA. Translation: BAE77461.1.
PIRiS30732.
RefSeqiNP_418284.1. NC_000913.3.
WP_001192396.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2OUGX-ray2.10A/B/C/D1-162[»]
ProteinModelPortaliP0AFW0.
SMRiP0AFW0. Positions 2-162.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP0AFW0. 7 interactions.
STRINGi511145.b3842.

Proteomic databases

PaxDbiP0AFW0.
PRIDEiP0AFW0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76845; AAC76845; b3842.
BAE77461; BAE77461; BAE77461.
GeneIDi948327.
KEGGiecj:JW3818.
eco:b3842.
PATRICi32123181. VBIEscCol129921_3956.

Organism-specific databases

EchoBASEiEB0832.
EcoGeneiEG10839. rfaH.

Phylogenomic databases

eggNOGiENOG4105MDZ. Bacteria.
COG0250. LUCA.
HOGENOMiHOG000272711.
InParanoidiP0AFW0.
KOiK05785.
OMAiNCLTPMI.
OrthoDBiEOG6KHG0C.

Enzyme and pathway databases

BioCyciEcoCyc:EG10839-MONOMER.
ECOL316407:JW3818-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AFW0.
PROiP0AFW0.

Family and domain databases

Gene3Di3.30.70.940. 1 hit.
HAMAPiMF_00951. RfaH.
InterProiIPR006645. NGN_dom.
IPR010215. Transcription_antiterm_RfaH.
[Graphical view]
PfamiPF02357. NusG. 1 hit.
[Graphical view]
SMARTiSM00738. NGN. 1 hit.
[Graphical view]
SUPFAMiSSF82679. SSF82679. 1 hit.
TIGRFAMsiTIGR01955. RfaH. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Escherichia coli HlyT protein, a transcriptional activator of haemolysin synthesis and secretion, is encoded by the rfaH (sfrB) locus required for expression of sex factor and lipopolysaccharide genes."
    Bailey M.J.A., Koronakis V., Schmoll T., Hughes C.
    Mol. Microbiol. 6:1003-1012(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    Strain: 5KC.
  2. Missiakas D., Georgopoulos C., Raina S.
    Submitted (MAR-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
    Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
    Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "RfaH enhances elongation of Escherichia coli hlyCABD mRNA."
    Leeds J.A., Welch R.A.
    J. Bacteriol. 178:1850-1857(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN HEMOLYSIN TRANSCRIPTION.
    Strain: 5KC.
  7. "Increased distal gene transcription by the elongation factor RfaH, a specialized homologue of NusG."
    Bailey M.J., Hughes C., Koronakis V.
    Mol. Microbiol. 22:729-737(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Enhancing transcription through the Escherichia coli hemolysin operon, hlyCABD: RfaH and upstream JUMPStart DNA sequences function together via a postinitiation mechanism."
    Leeds J.A., Welch R.A.
    J. Bacteriol. 179:3519-3527(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "RfaH and the ops element, components of a novel system controlling bacterial transcription elongation."
    Bailey M.J., Hughes C., Koronakis V.
    Mol. Microbiol. 26:845-851(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "In vitro recruitment of the RfaH regulatory protein into a specialised transcription complex, directed by the nucleic acid ops element."
    Bailey M.J., Hughes C., Koronakis V.
    Mol. Gen. Genet. 262:1052-1059(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  11. "The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand."
    Artsimovitch I., Landick R.
    Cell 109:193-203(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH DNA AND RNAP.
  12. "RfaH, a bacterial transcription antiterminator."
    Santangelo T.J., Roberts J.W.
    Mol. Cell 9:698-700(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  13. "The transcriptional antiterminator RfaH represses biofilm formation in Escherichia coli."
    Beloin C., Michaelis K., Lindner K., Landini P., Hacker J., Ghigo J.M., Dobrindt U.
    J. Bacteriol. 188:1316-1331(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN BIOFILM FORMATION, DISRUPTION PHENOTYPE.
    Strain: K12 / MG1655 / ATCC 47076.
  14. "Structural basis for converting a general transcription factor into an operon-specific virulence regulator."
    Belogurov G.A., Vassylyeva M.N., Svetlov V., Klyuyev S., Grishin N.V., Vassylyev D.G., Artsimovitch I.
    Mol. Cell 26:117-129(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), SUBUNIT, DOMAIN.

Entry informationi

Entry nameiRFAH_ECOLI
AccessioniPrimary (citable) accession number: P0AFW0
Secondary accession number(s): P26614, Q2M8E5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: May 11, 2016
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.