{PDOC51856}
{PS51856; RHO_RNA_BD}
{BEGIN}
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* Rho RNA-binding (RNA-BD) domain profile *
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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 beta-strands in
two antiparallel beta-sheets and a short alpha-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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: February 2018 / First entry.

[ 1] Allison T.J., Wood T.C., Briercheck D.M., Rastinejad F.,
     Richardson J.P., Rule G.S.
     "Crystal structure of the RNA-binding domain from transcription
     termination factor rho."
     Nat. Struct. Biol. 5:352-356(1998).
     PubMed=9586995
[ 2] Briercheck D.M., Wood T.C., Allison T.J., Richardson J.P., Rule G.S.
     "The NMR structure of the RNA binding domain of E. coli rho factor
     suggests possible RNA-protein interactions."
     Nat. Struct. Biol. 5:393-399(1998).
     PubMed=9587002
[ 3] Canals A., Uson I., Coll M.
     "The structure of RNA-free Rho termination factor indicates a dynamic
     mechanism of transcript capture."
     J. Mol. Biol. 400:16-23(2010).
     PubMed=20452362; DOI=10.1016/j.jmb.2010.05.004
[ 4] Banerjee S., Chalissery J., Bandey I., Sen R.
     "Rho-dependent transcription termination: more questions than
     answers."
     J. Microbiol. 44:11-22(2006).
     PubMed=16554712
[ 5] D'Heygere F., Rabhi M., Boudvillain M.
     "Phyletic distribution and conservation of the bacterial transcription
     termination factor Rho."
     Microbiology 159:1423-1436(2013).
     PubMed=23704790; DOI=10.1099/mic.0.067462-0

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