The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Mtr4-Air2-interaction site
Functional site description:
The TRAMP complex is involved in exosome-mediated degradation of aberrant RNAs and RNA surveillance in the nucleus. Oligo-adenylated tails are added to aberrant RNA substrates, thus marking them for degradation. In Fungi, it is formed by a RNA Helicase, Mtr4, in addition with a RNA-binding zinc knuckle protein, Air1/2 and a poly(A)polymerase, Trf4 or Trf5. The non-covalent binding of Trf4 and Mtr4 is mediated via a short motif, which interacts with the DExH core of Mtr4. The motif is conserved in Fungi.
ELM Description:
The RNA-binding zinc knuckle protein Air2 (Q12476) noncovalently interacts with the DExH core of Mtr4 (P47047, PF00270). The core motif consists of glycine, followed by arginine, tyrosine, phenylalanine and again glycine. This motif is conserved in Fungi. The arginine forms a salt bridge with a glutamic acid of Mtr4 as well as a cation-pi interaction with a tyrosine. The following tyrosine interacts with a hydrophobic pocket that is formed by a isoleucine and two leucines of Mtr4 (Falk,2014, 4U4C).
The same crystal structure work argues for interactions upstream of this sequence. Anyhow, these interacting amino acids are only conserved in budding yeast. This might explain why the TRAMP complex was found to be more stable in Saccharomyces cerevisiae than in Schizosaccharomyces pombe, which lacks these upstream interaction (Falk,2014, Keller,2010). In budding yeast, a short helix is formed upstream of the GRYFG core motif. Amino acids within this helix and upstream of it contribute to the interaction with Mtr4. Isoleucine and valine interact via hydrophobic contacts with a methionine on Mtr4. In some instances, a different hydrophobic amino acid can be found in place of isoleucine ([FYMV]). There are two positions between these interacting amino acids where any amino acid is supposedly allowed, frequently seen in the alignment these positions are negatively charged residues ([DE]). The following stretch forms the short helix, which fits against the helical bundle domain of Mtr4. After a stretch of five positions where any amino acid is allowed, a negatively charged amino acid, glutamic acid or aspartic acid must occur. In some instances in other yeast strains it seems possible that this position shifted, in which case the negatively charged amino acid occurs after a stretch of four amino acids and at the position thereafter any amino acid is allowed, followed by a leucine (Falk,2014). After a stretch of six positions where any amino acid is allowed the core motif GRYFG occurs.
Pattern: GRYFG
Pattern Probability: 9.059e-08
Present in taxon: Fungi
Interaction Domain:
DEAD (PF00270) DEAD/DEAH box helicase (Stochiometry: 1 : 1)
o See 3 Instances for LIG_Mtr4_Air2_1
o Abstract
RNA processing and surveillance is a mechanisms closely regulated. In general, RNAs are degraded when their function and use is completed, which means the lifetime of a RNA molecule depends on its type (e.g. long life time for rRNA; short for aberrant RNA). There are several possible pathways for the decay of RNA substrates; one of the major players for degradation and trimming in the nucleus is the exosome (Houseley,2009). Several cofactors (such as the TRAMP complex) are needed by the exosome for target recognition. The TRAMP complex consists of a RNA helicase (MTR4), a poly(A)polymerase (Trf4 or Trf5) and a RNA-binding zinc knuckle protein (Air1 or Air2). While Air1 or Air2 recognizes the RNA substrates, Mtr4 is responsible for unwinding the RNA in order for Trf4 or Trf5 to polyadenylate the substrate (LaCava,2005). This poly(A) tail can be recognized by the exosome, initiating the degradation of the substrate (Hamill,2010). The broad spectrum of possible RNA substrates for TRAMP consists of hypomodified or incorrectly folded tRNA, rRNA, snRNA and snoRNA, incorrectly folded or spliced pre-mRNA, cryptic unstable transcripts (CUTs) and defective pre-ribosomes (Kadaba,2004, Carneiro,2007, Houseley,2009, Wlotzka,2011).
The duplication of the polymerase Trf and the zinc knuckle protein Air arose due to a whole genome duplication event in Saccharomyces cerevisiae (15004568). The Air protein mediates RNA substrate specificity. While Air2 preferentially targets many snoRNAs, Air1 is involved in targeting mRNAs that are important in maintaining the 2μ plasmid (Schmidt,2012). Research also determined that Air1 or Air2 must be present in order for Trf4 to actively polyadenylate RNA substrates (LaCava,2005). Both Air2 and Trf4 non-covalently interact with the DexH-helicase core of Mtr4 (Falk,2014, PF00270). A study describing the crystal structure of Mtr4 in complex with a fragment of Air2 and Trf4 revealed a short motif responsible for protein interaction, which is conserved in Fungi (Falk,2014, 4U4C).
o 9 selected references:

o 10 GO-Terms:

o 3 Instances for LIG_Mtr4_Air2_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q9P795 air1
78 82 EWADVSRGRYFGSDPSESIV TP 2 Schizosaccharomyces pombe 972h-
P40507 AIR1
55 59 LRTLRGQGRYFGITDYDSNG TP 2 Saccharomyces cerevisiae S288c
Q12476 AIR2
43 47 LRALRGQGRYFGVSDDDKDA TP 7 Saccharomyces cerevisiae S288c
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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