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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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
ChainiPRO_00000972811 – 162Transcription antitermination protein RfaHAdd BLAST162

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 interactors.
STRINGi511145.b3842.

Structurei

Secondary structure

1162
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 9Combined sources7
Turni11 – 13Combined sources3
Helixi14 – 23Combined sources10
Beta strandi27 – 29Combined sources3
Beta strandi32 – 51Combined sources20
Beta strandi54 – 59Combined sources6
Turni61 – 63Combined sources3
Helixi66 – 71Combined sources6
Beta strandi75 – 78Combined sources4
Beta strandi81 – 85Combined sources5
Helixi91 – 98Combined sources8
Helixi118 – 129Combined sources12
Helixi135 – 155Combined sources21

3D structure databases

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

Family and domain databases

Gene3Di2.30.30.30. 1 hit.
3.30.70.940. 1 hit.
HAMAPiMF_00951. RfaH. 1 hit.
InterProiIPR006645. NGN_dom.
IPR014722. Rib_L2_dom2.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OUGX-ray2.10A/B/C/D1-162[»]
ProteinModelPortaliP0AFW0.
SMRiP0AFW0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP0AFW0. 7 interactors.
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.
OMAiNQGVECF.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP0AFW0.
PROiP0AFW0.

Family and domain databases

Gene3Di2.30.30.30. 1 hit.
3.30.70.940. 1 hit.
HAMAPiMF_00951. RfaH. 1 hit.
InterProiIPR006645. NGN_dom.
IPR014722. Rib_L2_dom2.
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...

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: November 30, 2016
This is version 91 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.