RNA recognition motif domain (IPR000504)

Short name: RRM_dom

Overlapping homologous superfamilies

Domain relationships


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 [PMID: 3072706, PMID: 3192525, PMID: 3313012]. 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 [PMID: 2470643, PMID: 2467746]. 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) [PMID: 3192525, PMID: 3313012, PMID: 2467746]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition [PMID: 15231733]. The motif also appears in a few single stranded DNA binding proteins.

The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta 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 [PMID: 8290338]. The RRM is reviewed in a number of publications [PMID: 1716386, PMID: 15853797, PMID: 16387655].

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0003676 nucleic acid binding

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE profiles