PROSITE documentation PDOC51856 [for PROSITE entry PS51856]

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.