The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Mtr4-Trf4-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 poly(A)polymerase, Trf4 or Trf5 and a RNA-binding zinc knuckle protein, Air1/2. 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.
ELMs with same func. site: LIG_Mtr4_Trf4_1  LIG_Mtr4_Trf4_2 
ELM Description:
The poly(A) polymerase Trf4 (P53632 or Trf5 P48561) binds to the DExH core (PF00270) of Mtr4 (P47047) via a short motif. A hydrophobic amino acid, most frequently leucine although all amino acids with hydrophobic side chains (except tyrosine) are allowed (alanine, valine, isoleucine, leucine, methionine, phenylalanine and trypthophan) is the first position. This is followed most frequently by a stretch of four positions where every amino acid is allowed, although there are occurrences where the hydrophobic amino acid shifted one position upstream or downstream. This is followed by the core motif. This highly conserved sequence consists of aspartic acid followed by phenyalalanine and isoleucine (Losh,2015, Falk,2014). Only rarely this sequence is slightly changed, as for example in a few yeast strains. Allowed substitutions are glutamic acid for aspartic acid, tyrosine for phenylalanine or leucine for isoleucine. Taking into account a crystal structure of Mtr4 interacting with a truncated, short Trf4 fragment (interaction of Mtr4 and short Air2 fragment is shown as well), one can argue for ring-interaction between the phenylalanine position and a tyrosine on the interacting protein (Mtr4). Additionally, the aspartic acid of the highly conserved sequence interacts via electrostatic and polar interactions with an arginine and an asparagine side chain of Mtr4 (Falk,2014, 4U4C). The next position downstream of the highly conserved sequence accepts serine, alanine, proline, lysine and glutamine. Interestingly, proline is accepted despite the fact that it disrupts possible H-bonds. This position is followed either by phenylalanine or leucine. After a stretch of 3 to 6 flexible positions where every amino acid is allowed (frequently, at least one of these positions is serine), a negatively charged sequence of at least 3 aspartic acids and/or glutamic acids follows.
Pattern: [LFVAIMW].{3,5}[DE][FY][IL][SAPGK][FL].{3,6}[DE]{3}
Pattern Probability: 1.441e-07
Present in taxon: Fungi
Interaction Domain:
DEAD (PF00270) DEAD/DEAH box helicase (Stochiometry: 1 : 1)
o See 4 Instances for LIG_Mtr4_Trf4_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 (Wlotzka,2011, Kadaba,2004, Carneiro,2007, Houseley,2009). Interestingly, the polyadenylation of stable mRNA by the canonical poly(A) polymerase PAP1 does not lead to degradation. The two pathways of modification therefore must be distinguishable. The length of the tail seems to be one way of encoding the addressed pathway. While the polyadenylation added by Trf4/5 is in a range of 10-50 nucleotides, PAP1 adds tails of 60-80 nucleotides (reviewed in Schmidt,2013). Furthermore, Mtr4 can modulate the activity of Trf4/5 in the TRAMP complex, resulting in a poly(A) tail length of only 3-5 nucleotides (Jia,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 non-covalent binding of Trf4 (P53632) and the DExH-helicase core of Mtr4 (P47047, PF00270) is mediated by the described motif, which is conserved in both Trf4 (P53632) and Trf5 (P48561) in Fungi. In Vertebrata, the motif for interaction between Mtr4 and PAPD5 (human homolog of Trf5 (Houseley,2009)) slightly changed. Interestingly, the motif occurs only on human PAPD5 but not on human PAPD7 or POLS (human homolog of Trf4 Houseley,2009). The potential motif in Vertebrata (proposed through multiple sequence alignment in Losh,2015 and investigated by curator based on alignments) is described in the entry (LIG_MTR4_TRF4_2). However, note that there is no experimental evidence for this motif in Vertebrata yet.
o 7 selected references:

o 8 GO-Terms:

o 4 Instances for LIG_Mtr4_Trf4_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
131 146 NALDDNQDFIGFSDSEEEVA TP 2 Ashbya gossypii ATCC 10895
P48561 TRF5
101 117 SLEDNQDFIAFSDSSEDETE TP 3 Saccharomyces cerevisiae S288c
Q9UTN3 cid14
150 168 VENNSDFIKFDWNSDEDEDS TP 3 Schizosaccharomyces pombe 972h-
P53632 PAP2
118 133 DLANNDDFISLSASSEDEQA TP 5 Saccharomyces cerevisiae S288c
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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