P0AFW0 (RFAH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcription antitermination protein RfaH

Gene names

Name:	rfaH
Synonyms:	hlyT, sfrB
Ordered Locus Names:	b3842, JW3818

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	162 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.1 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13
Subunit structure	Interacts with both the nontemplate DNA and the RNA polymerase (RNAP). Monomer in solution. Ref.11 Ref.14
Domain	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. Ref.14
Disruption phenotype	Inactivation results in increased initial adhesion and biofilm formation. Ref.13
Sequence similarities	Belongs to the RfaH family.

Ontologies

Keywords
Biological process	Transcription Transcription antitermination Transcription regulation
Ligand	DNA-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	positive regulation of transcription elongation from RNA polymerase II promoter Inferred from electronic annotation. Source: InterPro transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding transcription antitermination factor activity Inferred from direct assay PubMed 7007352. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 162

162

Transcription antitermination protein RfaH HAMAP-Rule MF_00951

PRO_0000097281

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

162

Helix Strand Turn

Details...

Beta strand

3 – 9

7

Turn

11 – 13

3

Helix

14 – 23

10

Beta strand

27 – 29

3

Beta strand

32 – 51

20

Beta strand

54 – 59

6

Turn

61 – 63

3

Helix

66 – 71

6

Beta strand

75 – 78

4

Beta strand

81 – 85

5

Helix

91 – 98

8

Helix

118 – 129

12

Helix

135 – 155

21

Sequences

	Sequence		Length	Mass (Da)
	P0AFW0 [UniParc]. Last modified December 20, 2005. Version 1. Checksum: 2A298947EBB58C65	FASTA	162	18,340
	10 20 30 40 50 60 MQSWYLLYCK RGQLQRAQEH LERQAVNCLA PMITLEKIVR GKRTAVSEPL FPNYLFVEFD 70 80 90 100 110 120 PEVIHTTTIN ATRGVSHFVR FGASPAIVPS AVIHQLSVYK PKDIVDPATP YPGDKVIITE 130 140 150 160 GAFEGFQAIF TEPDGEARSM LLLNLINKEI KHSVKNTEFR KL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

S30732.

RefSeq

NP_418284.1. NC_000913.2.
YP_491602.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2OUG	X-ray	2.10	A/B/C/D	1-162	[»]

ProteinModelPortal

P0AFW0.

SMR

P0AFW0. Positions 2-162.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0AFW0. 7 interactions.

STRING

511145.b3842.

Proteomic databases

PaxDb

P0AFW0.

PRIDE

P0AFW0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76845; AAC76845; b3842.
BAE77461; BAE77461; BAE77461.

GeneID

12934471.
948327.

KEGG

ecj:Y75_p3338.
eco:b3842.

PATRIC

32123181. VBIEscCol129921_3956.

Organism-specific databases

EchoBASE

EB0832.

EcoGene

EG10839. rfaH.

Phylogenomic databases

eggNOG

COG0250.

HOGENOM

HOG000272711.

KO

K05785.

OMA

GCKELMT.

ProtClustDB

PRK09014.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10839-MONOMER.
ECOL316407:JW3818-MONOMER.

Gene expression databases

Genevestigator

P0AFW0.

Family and domain databases

Gene3D

3.30.70.940. 1 hit.

HAMAP

MF_00951. RfaH.

InterPro

IPR005824. KOW.
IPR010215. Transcription_activator_RfaH.
IPR006645. Transcrpt_antiterm_NusG_N.
[Graphical view]

Pfam

PF02357. NusG. 1 hit.
[Graphical view]

SMART

SM00739. KOW. 1 hit.
SM00738. NGN. 1 hit.
[Graphical view]

SUPFAM

SSF82679. Transcrpt_antiterm_NusG_N. 1 hit.

TIGRFAMs

TIGR01955. RfaH. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0AFW0.

Entry information

Entry name

RFAH_ECOLI

Accession

Primary (citable) accession number: P0AFW0
Secondary accession number(s): P26614, Q2M8E5

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	December 20, 2005
Last modified:	May 29, 2013
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program