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RNA recognition motif
RNA recognition motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is a protein domain which main function is single-stranded RNA binding.

Structure
RRMs are small domains of approximately 90 amino acids. Typical RRM consists of four beta strands and two alpha helices arranged in a β1-α1-β2-β3-α2-β4 fold, where four antiparallel beta stands in the order β4-β1-β3-β2 create a beta sheet and two alpha helices are packed against it. In the central area of beta sheet two highly conserved regions are located. First, called RNP1 is located in β3 strand and constituted of eight amino acids: Lys/Arg-Gly-Phe/Tyr-Gly/Ala-Phe/Tyr-Val/Ile/Leu-X-Phe/Tyr where X can be any amino acid. Second region, called RNP2 is less conserved and was characterised as sequence of six amino acids: Ile/Val/Leu-Phe/Tyr-Ile/Val/Leu-X-Asn-Leu located in the β1 stand. Both sequences play important roles in ligand binding. Loops between alpha-helices and beta-strands as well as N- and C-termianal regions near RRM usually remain disordered but can sometimes create secondary structure elements and often take part in RNA recognition.

Multiple RRMs
In prokaryotic organisms only one RRM domain can be found in one protein. In eukaryotic organisms about 44% of proteins containing RRM is composed of two to six RRMs. Neighbouring RRM domains can be used to recognise long RNA sequences (8-10 nucleotides) and to increase binding affinity and specificity. In some proteins interactions between RRMs can produce loops in their bound RNA or prevent RNA binding.

RNA recognition
Known RRM domains recognise single stranded RNA from minimum 2 to maximum 8 nucleotides long. For many RRMs mechanism of ligand binding is similar and involves highly conserved aromatic residues of RNP1 and RNP2. Most commonly two nucleobases from neighbouring nucleotides of RNA interact with aromatic rings located in the position 2 of RNP2 and position 5 of RNP1 and the aromatic ring located in position 3 of RNP1 stacks between two sugar rings of RNA. In other cases different residues of beta-sheet, loops between secondary structure elements and additional N- and C- terminal regions are involved in ligand binding. Although mechanism of ligand binding is well established for many RRMs, universal code that could explain relationship between RRM structure and its ligand sequence remains unknown.

Abundance
Proteins containing RRM are present in organisms of all live kingdoms. RRMs are quite rare in prokaryotes and are one of the most abundant domains in eukaryotes. Up to now (December 2013) more then 1 000 sequences coding RRM domain in prokaryotic organisms are know and more than 30 000 in eukaryotic organisms. In Homo Sapiens genome there are 812 sequences coding RRM. Approximately 0,5-1% of human proteins have at least one RRM domain.

Role in cell
RRM containing proteins take part in all cellular processes involving RNA processing and transport, such as: transcription, splicing (e.g.,SR proteins), alternative splicing (e.g.,RBFOX, SR proteins), 5'-capping and 3'-polyadenylation (e.g.,CSTF2), RNA editing (e.g.,ACF), mRNA export (e.g.,TLS), translation (e.g., eIF4B), RNA degradation

Protein interaction
It is known that some RRMs have not only the ability to bind RNA but are also involved in protein-protein interactions. Three classes of interactions between RRMs and proteins can be distinguished: Two RRMs usually interact to form an extended surface for RNA binding (e.g., two N-terminal RRMs of hnRNPA1) which would be able to recognise longer RNA sequence, increase binding affinity and specificity. RRM-RRM interaction can also prevent RNA binding or produce additional loops in RNA structure. Interaction with another protein can regulate RRMs ability to associate with RNA. Some proteins (e.g., CBP20) can bind its ligand only in contact with another protein. There are known some protein containing RRM that are involved in protein-protein interactions and can be part of big protein complexes but do not associate with RNA (e.g., Y14)
 * between RRM and RRM
 * between RRM which binds RNA and another protein
 * between to RRM which does not bind RNA and another protein

qRRM
Quasi RRMs are protein domains similar to RRMs but have poorly conserved RNP1 and RNP2 sequences. To bind RNA they use loops between the secondary structure elements instead of beat-sheet. qRRMs are present in hnRNP F/H family.They are known to recognise G-track in RNA and take part in regulating alternative splicing.