The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Trf4 PAP-associated domain ligand
Functional site description:
The Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) RNA quality control complex is a key player in RNA surveillance. Within this complex Air1/2 employs its 5th zinc knuckle and a conserved IWRxY motif within the linker connecting the 4th and 5th zinc knuckles for binding Trf4, while other regions of the protein (including an MTR4 arch domain-interacting (AIM) motif) contact Mtr4, thus ultimately fulfilling a bridging function within the complex. The motif is present in the close paralogs Air1 and Air2 and it seems to be strictly conserved from yeasts to human, since it is also present in the human ortholog ZCCHC7.
ELM Description:
The IWRxY motif is located at the beginning of the linker between the 4th and 5th zinc knuckles of Air1/2, right after the 4th zinc knuckle (Fasken,2011; Hamill,2010). The conserved starting Ile residue of the motif is only separated by two residues from the last Cys of the 4th zinc knuckle. This is probably the reason why, although the motif resides within a linker, it is not predicted to be natively disordered.
In the complex (3NYB) between yeast Air2 (Q12476) and Trf4 (P53632) the motif is partly helical, a helix is formed by part of the 4th zinc knuckle, the residues separating it from the motif and the first two residues of the motif I139 and the conserved W140 (UniProt numbering). W140 fits into a hydrophobic pocket, while the first residue after the helix, R141 coordinates several salt bridges with both E378 and E381 of Trf4. With the following residue, A142, the Air2 chain turns back and the following conserved Y143 forms a hydrogen bond with the sidechain of E378 of Trf4 through its OH group (so a change to Phe in this position would destroy this contact; Hamill,2010). L145 also makes hydrophobic contacts and it is highly conserved in yeasts and in vertebrates, except for S. pombe Air1. The structural features of the bound motif are in good agreement with the alignments of Air1 and Air2 showing that while the I139 position has slight sequence variability among similarly sized hydrophobic residues Ile, Leu and Val, the W140, R141 and Y143 positions are strictly conserved in all the species.

Pattern: [IVL]WR.Y
Pattern Probability: 8.990e-07
Present in taxon: Eukaryota
Interaction Domain:
PAP/25A-associated (IPR002058) This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity (Stochiometry: 1 : 1)
o See 4 Instances for LIG_Trf4_IWRxY_1
o Abstract
The Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex is a major player in RNA surveillance and decay pathways. The TRAMP complex can be considered as a nuclear exosome cofactor that recruits the exosome to degrade certain unwanted RNA species (Fasken,2011).

Within the complex, the RNA-binding protein Air1/2 performs a bridging function between the poly(A) polymerase (Trf4/5) and RNA helicase (Mtr4) subunits (Holub,2012). Air1/2 interacts with Trf4 through its 4th and 5th zinc knuckles and a conserved IWRxY motif at the beginning of the linker connecting them (Fasken,2011; Holub,2012), while other regions of the protein (including an N-terminal MTR4 arch domain-interacting (AIM) motif LIG_MTR4_AIM_1) contact Mtr4 (Falk,2014). The motif is present in the close paralogs Air1 and Air2 and it seems to be strictly conserved from yeasts to human, as it is also present in the human ortholog ZCCHC7 that is known to interact with PAPD5 and PAPD7, the human orthologs of Trf4 (Fasken,2011). Human TRAMP-like proteins are involved in the turnover of pre-rRNA 5'ETS fragments (Sudo,2016). In S. pombe there is a single TRAMP-like complex that consists of Mtr4, Cid14, and Air1 (Keller,2010).

The Trf4p surface bound by the Air2 motif and zinc knuckle is highly conserved in a wide range of eukaryotes (Hamill,2010). There is a structure available for the complex (3NYB) between yeast Air2 (Q12476) and Trf4 (P53632) which justifies the high conservation of the IWRxY residues, since they mediate various contacts with Trf4 (Hamill,2010). The full interaction surface with Trf4 is considerably larger than the motif interface. While the 4th zinc knuckle (residues 123–136) is only tethered to Trf4p via the adjacent motif and has little direct contact with Trf4p, the 5th zinc knuckle makes an extensive interaction. The motif and the 5th knuckle are separated by a flexible linker not visible in the structure (Hamill,2010). Mutations to Zn knuckles 4 or 5 or the IWRxY motif in Air1 or 2 cause temperature-sensitive growth defects in S. cerevisiae, most probably through compromising the integrity of the TRAMP complex (Fasken,2011; Holub,2012).
o 4 selected references:

o 12 GO-Terms:

o 4 Instances for LIG_Trf4_IWRxY_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q12476 AIR2
139 143 SKERCPSIWRAYILVDDNEK TP 3 Saccharomyces cerevisiae S288c
322 326 YTDACTEIWRQYHLTTKPGP TP 1 Homo sapiens (Human)
Q9P795 air1
169 173 TSSTCPLIWRYYVEKEHPVR TP 6 Schizosaccharomyces pombe 972h-
P40507 AIR1
152 156 SRERCPSIWRSYLLKTKDAN TP 4 Saccharomyces cerevisiae S288c
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement