DSRM

Double-stranded RNA binding motif

• SMART accession number: SM00358
• Interpro abstract (IPR001159): The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions [(PUBMED:8036511)]. It is involved in localisation of at least five different mRNAs in the early Drosophila embryo and by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.
• GO component: intracellular (GO:0005622)
• GO function: double-stranded RNA binding (GO:0003725)

There are 4241 DSRM domains in 3061 proteins in SMART's nrdb database.

Cellular role (predicted cellular role)

Binding / catalysis: RNA binding

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Mian IS
• Comparative sequence analysis of ribonucleases HII, III, II PH and D.
• Nucleic Acids Res. 1997; 25: 3187-95

Escherichia coli ribonucleases (RNases) HII, III, II, PH and D have been used to characterise new and known viral, bacterial, archaeal and eucaryotic sequences similar to these endo- (HII and III) and exoribonucleases (II, PH and D). Statistical models, hidden Markov models (HMMs), were created for the RNase HII, III, II and PH and D families as well as a double-stranded RNA binding domain present in RNase III. Results suggest that the RNase D family, which includes Werner syndrome protein and the 100 kDa antigenic component of the human polymyositis scleroderma (PMSCL) autoantigen, is a 3'-->5' exoribonuclease structurally and functionally related to the 3'-->5' exodeoxyribonuclease domain of DNA polymerases. Polynucleotide phosphorylases and the RNase PH family, which includes the 75 kDa PMSCL autoantigen, possess a common domain suggesting similar structures and mechanisms of action for these 3'-->5' phosphorolytic enzymes. Examination of HMM-generated multiple sequences alignments for each family suggest amino acids that may be important for their structure, substrate binding and/or catalysis.

• Zamore PD, Williamson JR, Lehmann R
• The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins.
• RNA. 1997; 3: 1421-33

Translation of hunchback(mat) (hb[mat]) mRNA must be repressed in the posterior of the pre-blastoderm Drosophila embryo to permit formation of abdominal segments. This translational repression requires two copies of the Nanos Response Element (NRE), a 16-nt sequence in the hb[mat] 3' untranslated region. Translational repression also requires the action of two proteins: Pumilio (PUM), a sequence-specific RNA-binding protein; and Nanos, a protein that determines the location of repression. Binding of PUM to the NRE is thought to target hb(mat) mRNA for repression. Here, we show the RNA-binding domain of PUM to be an evolutionarily conserved, 334-amino acid region at the carboxy-terminus of the approximately 158-kDa PUM protein. This contiguous region of PUM retains the RNA-binding specificity of full-length PUM protein. Proteins with sequences homologous to the PUM RNA-binding domain are found in animals, plants, and fungi. The high degree of sequence conservation of the PUM RNA-binding domain in other far-flung species suggests that the domain is an ancient protein motif, and we show that conservation of sequence reflects conservation of function: that is, the homologous region from a human protein binds RNA with sequence specificity related to but distinct from Drosophila PUM.

• Burd CG, Dreyfuss G
• Conserved structures and diversity of functions of RNA-binding proteins.
• Science. 1994; 265: 615-21

In eukaryotic cells, a multitude of RNA-binding proteins play key roles in the posttranscriptional regulation of gene expression. Characterization of these proteins has led to the identification of several RNA-binding motifs, and recent experiments have begun to illustrate how several of them bind RNA. The significance of these interactions is reflected in the recent discoveries that several human and other vertebrate genetic disorders are caused by aberrant expression of RNA-binding proteins. The major RNA-binding motifs are described and examples of how they may function are given.

• StJohnston D, Brown NH, Gall JG, Jantsch M
• A conserved double-stranded RNA-binding domain.
• Proc Natl Acad Sci U S A. 1992; 89: 10979-83

We have identified a double-stranded (ds)RNA-binding domain in each of two proteins: the product of the Drosophila gene staufen, which is required for the localization of maternal mRNAs, and a protein of unknown function, Xlrbpa, from Xenopus. The amino acid sequences of the binding domains are similar to each other and to additional domains in each protein. Database searches identified similar domains in several other proteins known or thought to bind dsRNA, including human dsRNA-activated inhibitor (DAI), human trans-activating region (TAR)-binding protein, and Escherichia coli RNase III. By analyzing in detail one domain in staufen and one in Xlrbpa, we delimited the minimal region that binds dsRNA. On the basis of the binding studies and computer analysis, we have derived a consensus sequence that defines a 65- to 68-amino acid dsRNA-binding domain.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
70.00	map00791	Atrazine degradation
20.00	map00230	Purine metabolism
10.00	map03010	Ribosome

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with DSRM domain which could be assigned to a KEGG orthologous group, and not all proteins containing DSRM domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of DSRM domains in PDB

PDB code	Title
1di2	Crystal structure of a dsrna-binding domain complexed with dsrna: molecular basis of double-stranded rna-protein interactions
1ekz	Nmr structure of the complex between the third dsrbd from drosophila staufen and a rna hairpin
1o0w	Crystal structure of ribonuclease iii (tm1102) from thermotoga maritima at 2.0 a resolution
1qu6	Structure of the double-stranded rna-binding domain of the protein kinase pkr reveals the molecular basis of its dsrna-mediated activation
1rc7	Crystal structure of rnase iii mutant e110k from aquifex aeolicus complexed with ds-rna at 2.15 angstrom resolution
1stu	Double stranded rna binding domain
1t4l	Solution structure of double-stranded rna binding domain of s. cerevisiae rnase iii (rnt1p) in complex with the 5' terminal rna hairpin of snr47 precursor
1t4n	Solution structure of rnt1p dsrbd
1t4o	Crystal structure of rnt1p dsrbd
1uhz	Solution structure of dsrna binding domain in staufen homolog 2
1uil	Double-stranded rna-binding motif of hypothetical protein bab28848
1whn	Solution structure of the dsrbd from hypothetical protein bab26260
1whq	Solution structure of the n-terminal dsrbd from hypothetical protein bab28848
1x47	Solution structure of dsrm domain in dgcr8 protein
1x48	Solution structure of the second dsrm domain in interferon- induced, double-stranded rna-activated protein kinase
1x49	Solution structure of the first dsrm domain in interferon- induced, double-stranded rna-activated protein kinase
1yyk	Crystal structure of rnase iii from aquifex aeolicus complexed with double-stranded rna at 2.5-angstrom resolution
1yyo	Crystal structure of rnase iii mutant e110k from aquifex aeolicus complexed with double-stranded rna at 2.9- angstrom resolution
1yyw	Crystal structure of rnase iii from aquifex aeolicus complexed with double stranded rna at 2.8-angstrom resolution
1yz9	Crystal structure of rnase iii mutant e110q from aquifex aeolicus complexed with double stranded rna at 2.1- angstrom resolution
2a11	Crystal structure of nuclease domain of ribonuclase iii from mycobacterium tuberculosis
2b7t	Structure of adar2 dsrbm1
2b7v	Structure of adar2 dsrbm2
2cpn	Solution structure of the second dsrbd of tar rna-binding protein 2
2dix	Solution structure of the dsrm domain of protein activator of the interferon-induced protein kinase
2dmy	Solution structure of dsrm domain in spermatid perinuclear rna-bind protein
2ez6	Crystal structure of aquifex aeolicus rnase iii (d44n) complexed with product of double-stranded rna processing
2nue	Crystal structure of rnase iii from aquifex aeolicus complexed with ds-rna at 2.9-angstrom resolution
2nuf	Crystal structure of rnase iii from aquifex aeolicus complexed with ds-rna at 2.5-angstrom resolution
2nug	Crystal structure of rnase iii from aquifex aeolicus complexed with ds-rna at 1.7-angstrom resolution
2yt4	Crystal structure of human dgcr8 core
3c4b	Structure of rnaseiiib and dsrna binding domains of mouse dicer
3c4t	Structure of rnaseiiib and dsrna binding domains of mouse dicer
3htx	Crystal structure of small rna methyltransferase hen1

Links (links to other resources describing this domain)

• PFAM: dsrm
• INTERPRO: IPR001159