PROSITE documentation PDOC50137

Double stranded RNA-binding domain (dsRBD) profile

Description

In contrast to other RNA-binding domains, the about 65 amino acids long dsRBD domain [1,2,3] has been found in a number of proteins that specifically recognize double-stranded RNAs. The dsRBD domain is also known as DSRM (Double-Stranded RNA-binding Motif). dsRBD proteins are mainly involved in posttranscriptional gene regulation, for example by preventing the expression of proteins or by mediating RNAs localization. This domain is also found in RNA editing proteins. Interaction of the dsRBD with RNA is unlikely to involve the recognition of specific sequences [1,4,5,6]. Nevertheless, multiple dsRBDs may be able to act in combination to recognize the secondary structure of specific RNAs (i.e. Staufen) [1]. NMR analysis of the third dsRBD of Drosophila Staufen have revealed an α-β-β-β-α structure [7].

Some proteins known to include this domain are listed below.

  • Mammalian double-stranded RNA adenosine deaminase (DRADA) (EC 3.5.-.-), deaminates multiple adenosines to inosines by a hydrolytic deamination reaction only on double-stranded RNA; editates the messenger RNAs for glutamate receptor (GLUR) subunits (4 times).
  • Mammalian RNA-specific editase 1 (RED1), edits the messenger RNAs for glutamate receptor (GLUR) subunits (4 times).
  • Vertebrate TRBP, a protein that binds in vitro to the TAR stem-loop of human immunodeficiency virus (HIV) RNA (5 times).
  • Mammalian dsRNA-dependent p68 kinase (DAI, TIK) (EC 2.7.11.1), an interferon-induced protein that is involved in the cellular defense against viral infection.
  • Animal ATP-dependent RNA helicase A.
  • Human son protein.
  • Drosophila maleless protein. It associates with the X chromosome to regulate dosage compensation. It probably unwinds double-stranded DNA and RNA.
  • Drosophila Staufen, a developmental protein that associate specifically with Oskar and bicoid mRNAs, and is required for their localization to opposite poles in the egg.
  • S.pombe Pac-1 protein which digests double stranded-RNAs into short oligonucleotide. Identified as a suppressor of meiosis.
  • Bacterial RNase III (EC 3.1.26.3), an endonuclease that digest dsRNAs.
  • Viral E3L, a Vaccina virus protein which inhibits the p68 kinase activity, maybe by competing for dsRNA.
Note:

Not all RNase III proteins are picked-up by this motif, because of their high divergence.

Last update:

December 2001 / First entry.

Technical section

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

DS_RBD, PS50137; Double stranded RNA-binding domain (dsRBD) profile  (MATRIX)
Sequences known to belong to this class detected by the profile: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
• Domain architecture view of Swiss-Prot proteins matching PS50137
PS50137
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50137
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50137
• Scan Swiss-Prot/TrEMBL entries against PS50137
• view ligand binding statistics
Matching PDB structures: 1DI2 1EKZ 1O0W 1QU6 ... [ALL]

References

1 Authors St Johnston D., Brown N.H., Gall J.G., Jantsch M.
Source Proc. Natl. Acad. Sci. U.S.A. 89:10979-10983(1992).
2 Authors Burd C.G., Dreyfuss G.
Title Conserved structures and diversity of functions of RNA-binding proteins.
Source Science 265:615-621(1994).
PubMed ID 8036511
3 Authors Kim U., Wang Y., Sanford T., Zeng Y., Nishikura K.
Title Molecular cloning of cDNA for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing.
Source Proc. Natl. Acad. Sci. U.S.A. 91:11457-11461(1994).
PubMed ID 7972084
4 Authors Manche L., Green S.R., Schmedt C., Mathews M.B.
Title Interactions between double-stranded RNA regulators and the protein kinase DAI.
Source Mol. Cell. Biol. 12:5238-5248(1992).
PubMed ID 1357546
5 Authors Polson A.G., Bass B.L.
Title Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase.
Source EMBO J. 13:5701-5711(1994).
PubMed ID 7527340
6 Authors Schweisguth D.C., Chelladurai B.S., Nicholson A.W., Moore P.B.
Title Structural characterization of a ribonuclease III processing signal.
Source Nucleic Acids Res. 22:604-612(1994).
PubMed ID 8127710
7 Authors Bycroft M., Grunert S., Murzin A.G., Proctor M., St Johnston D.
Title NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5.
Source EMBO J. 14:3563-3571(1995).
PubMed ID 7628456

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