D
IPR000504

RNA recognition motif domain

InterPro entry
Short nameRRM_dom
Overlapping
homologous
superfamilies
 
domain relationships

Description

Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs
[9, 5, 6]
. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence
[8, 7]
. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu)
[5, 6, 7]
. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition
[1]
. The motif also appears in a few single stranded DNA binding proteins.

The typical RRM consists of four anti-parallel β-strands and two α-helices arranged in a β-α-β-β-α-β fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases
[10]
. The RRM is reviewed in a number of publications
[2, 3, 4]
.

This entry also includes some bacterial putative RNA-binding proteins.

References

1.U2AF homology motifs: protein recognition in the RRM world. Kielkopf CL, Lucke S, Green MR. Genes Dev. 18, 1513-26, (2004). View articlePMID: 15231733

2.RNA recognition: towards identifying determinants of specificity. Kenan DJ, Query CC, Keene JD. Trends Biochem. Sci. 16, 214-20, (1991). View articlePMID: 1716386

3.The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. Maris C, Dominguez C, Allain FH. FEBS J. 272, 2118-31, (2005). View articlePMID: 15853797

4.Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen. Teplova M, Yuan YR, Phan AT, Malinina L, Ilin S, Teplov A, Patel DJ. Mol. Cell 21, 75-85, (2006). View articlePMID: 16387655

5.Genomic structure and amino acid sequence domains of the human La autoantigen. Chambers JC, Kenan D, Martin BJ, Keene JD. J. Biol. Chem. 263, 18043-51, (1988). View articlePMID: 3192525

6.A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability. Sachs AB, Davis RW, Kornberg RD. Mol. Cell. Biol. 7, 3268-76, (1987). View articlePMID: 3313012

7.A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein. Query CC, Bentley RC, Keene JD. Cell 57, 89-101, (1989). View articlePMID: 2467746

8.RNA-binding proteins as developmental regulators. Bandziulis RJ, Swanson MS, Dreyfuss G. Genes Dev. 3, 431-7, (1989). View articlePMID: 2470643

9.Heterogeneous nuclear ribonucleoprotein particles and the pathway of mRNA formation. Dreyfuss G, Swanson MS, Pinol-Roma S. Trends Biochem. Sci. 13, 86-91, (1988). View articlePMID: 3072706

10.Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Birney E, Kumar S, Krainer AR. Nucleic Acids Res. 21, 5803-16, (1993). View articlePMID: 8290338

GO terms

biological process

  • None

molecular function

cellular component

  • None

Cross References

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