PROSITE documentation PDOC51856
Rho RNA-binding (RNA-BD) domain profile


The Rho factor is a ring-shaped ATP-dependent homo-hexameric helicase that mediates transcription termination in most prokaryotic cells by disengaging the transcription elongation complex formed by the RNA polymerase, DNA, and the nascent RNA transcript. Rho binds either single-stranded DNA or RNA with similar affinities and has the highest affinity towards cytidine-containing nucleic acids. Remarkably, Rho becomes activated only when it is bound to RNA. Rho protomers have an RNA-binding region at the N-terminus linked by a connector loop to a C-terminal ATPase domain. The RNA binding region comprises a variable N-terminal helix bundle (NHBD) domain and a core RNA-binding domain which forms the primary RNA binding site [1,2,3,4,5].

The core rho RNA-binding domain (RNA-BD), consisting of five β-strands in two antiparallel β-sheets and a short α-helix, is topologically similar to the oligonucleotide/oligosaccharide (OB) fold (see <PDB:1A62>). Within the core rho RNA-binding domain, there is an RNP-1 like sequence motif which is common to a large number of DNA- and RNA-binding proteins [1,2,3].

The profile we developed covers the entire core Rho RNA-binding domain.

Last update:

February 2018 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

RHO_RNA_BD, PS51856; Rho RNA-binding domain profile  (MATRIX)


1AuthorsAllison T.J. Wood T.C. Briercheck D.M. Rastinejad F. Richardson J.P. Rule G.S.
TitleCrystal structure of the RNA-binding domain from transcription termination factor rho.
SourceNat. Struct. Biol. 5:352-356(1998).
PubMed ID9586995

2AuthorsBriercheck D.M. Wood T.C. Allison T.J. Richardson J.P. Rule G.S.
TitleThe NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions.
SourceNat. Struct. Biol. 5:393-399(1998).
PubMed ID9587002

3AuthorsCanals A. Uson I. Coll M.
TitleThe structure of RNA-free Rho termination factor indicates a dynamic mechanism of transcript capture.
SourceJ. Mol. Biol. 400:16-23(2010).
PubMed ID20452362

4AuthorsBanerjee S. Chalissery J. Bandey I. Sen R.
TitleRho-dependent transcription termination: more questions than answers.
SourceJ. Microbiol. 44:11-22(2006).
PubMed ID16554712

5AuthorsD'Heygere F. Rabhi M. Boudvillain M.
TitlePhyletic distribution and conservation of the bacterial transcription termination factor Rho.
SourceMicrobiology 159:1423-1436(2013).
PubMed ID23704790

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