The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Nrd1 interaction motif
Functional site description:
The Nrd1 interaction motif (NIM) of Trf4 binds to the CTD-interacting domain (CID) of Nrd1 and thus stimulates the polyadenylation activity of the Trf4-Air2-Mtr4 (TRAMP) complex. Noncoding RNAs are targeted by the Nrd1-Nab3-Sen1 (NNS) complex for exosome-dependent degradation. The TRAMP complex recognizes and polyadenylates the RNAs targeted by the NNS complex for degradation or processing in the exosome. The TRAMP complex is formed by a poly(A) polymerase, Trf4 or Trf5, a RNA Helicase Mtr4, and a RNA-binding zinc knuckle protein, Air1/2.
ELM Description:
The poly(A) polymerase Trf4 binds to the CTD-interacting domain (CID) of Nrd1 via a short motif, consisting of a conserved negatively charged stretch in an N-terminal region and a hydrophobic β turn in the C-terminal region (Tudek,2014)(2MOW:A). This recognition mechanism is similar to the recognition of CID to phosphorylated CTD of RNAPII (2LO6:A). However, the binding affinity of NIM to CID is 100-fold stronger than the binding affinity of CTD to CID. Similar to the CTD, NIM forms a β turn at N580-P581-Y582-T583. P581, Y582 and Y579 dock into a hydrophobic pocket of CID lined by residues I29, T67, M126, L127 and I130. Additionally, Y579 interacts with P581 via intramolecular stacking. Y579 and P581 are very conserved amino acids in budding yeast and cannot be replaced. Y579 also interacts with a conserved D70 of CID by a hydrogen bond. The N-terminal region consists of the negatively charged residues D573-D574-D575-E576-D577 and binds to a positively charged pocket formed by K21, S25 and R28. Additionally, D577 and D575 of NIM form hydrogen bonds to S25 and R28 of CID. Furthermore, D573 of NIM forms a hydrogen bond with K21 of CID. The first three N-terminal positions can also be replaced by E. Position two and three can also accept a N residue. The 4th position (D577) is very conserved. The 5th position can either be a G or N or D. The next position (Y579) is very conserved. The next amino acid can be quite variable, whereas the following P581 is very conserved. The subsequent hydrophobic stretch can contain variable residues (Tudek,2014).

At the time of entry preparation, there was only experimental evidence for the existence of the NIM motif from a single species S. cerevisiae. The NIM motif is remarkably poorly conserved compared to other species of yeast and fungi. Assuming that the interaction is found in other species, this indicates that the motif sequence is evolving very fast, even by the standards of linear motifs. The other yeast homologues of Trf4 do not contain the motif.
Pattern: [DE][DEN][DEN]D[GDN]Y.P..
Pattern Probability: 4.399e-08
Present in taxon: Fungi
Interaction Domain:
CID domain (IPR006569) The C-terminal domain (CTD) of the large subunit of RNA polymerase II is a platform for mRNA processing factors and links gene transcription to mRNA capping, splicing and polyadenylation. CTD recognition is dependent on the phosphorylation state of the CTD itself, which varies during the course of transcription but has also been linked to the isomerization state of the CTD's proline residues. Several RNA-processing factors recognise the CTD by means of a conserved CTD-interacting domain (CID). Factors with CID domains include the serine/arginine-rich-like factors SCAF4 and SCAF8, Nrd1 (which is implicated in polyadenylation-independent RNA 3'-end formation) and Pcf11. Pcf11 is a conserved and essential subunit of the yeast cleavage factor 1A, which is required for 3'-RNA processing and transcription termination [, ]. The CID domain is a right-handed superhelix of eight alpha-helices forming a compact domain. The CID fold closely resembles that of VHS domains and is related to armadillo-repeat proteins, except for the two amino-terminal helices. Amino acid residues in the hydrophobic core of the domain are highly conserved across CID domains [, ]. (Stochiometry: 1 : 1)
o See 1 Instance for LIG_CID_NIM_1
o Abstract
The Nrd1-Nab3-Sen1 (NNS) complex controls pervasive transcription and is essential for the generation of sn/snoRNAs in S. cerevisiae. The NNS complex terminates transcription by RNA polymerase II (RNAPII) of noncoding RNAs, essentially for incorrectly folded rRNA and tRNA, snRNAs, snoRNAs and CUTs (cryptic unstable transcripts) (Tudek,2014, Kadaba,2004, Houseley,2009). The Trf4-Air2-Mtr4 (TRAMP) complex polyadenylates noncoding RNAs and thus targets the transcripts for trimming or complete degradation by the nuclear exosome. The TRAMP complex is composed of a DexH-box RNA helicase Mtr4, a poly(A) polymerase (Trf4 or Trf5) and a zinc knuckle RNA-binding protein (Air1 or Air2) (Falk,2014). The poly(A) polymerase targets aberrant RNA by adding a 3’-end poly(A) tail. This mechanism is contrary to the role of canonical nuclear polyadenylation of mRNAs that stimulates mRNA stability, transport from the nucleus and translation. For instance, the eukaryotic canonical poly(A) polymerase I (PAP I) protects newly transcribed pre-mRNA by adding a poly(A) tail (Falk,2014, Schmidt,2013). Although Trf4 contains the nucleotidyl transferase motif, the polyadenylation activity is only observed in TRAMP complexes containing Air1/2, because Trf4 has no RNA-binding domain (15828860). Additionally, the Air proteins modulate the interaction between Mtr4 and Trf4. Mtr4 is needed for the poly(A) polymerase activity and mediates the exosome activity in vitro (Schmidt,2013). The interaction of TRAMP with the NNS complex promotes RNA degradation by the exosome. As a result, the NNS complex has two mutually exclusive functions: one associated with termination of transcription and one associated with degradation of RNA (Tudek,2014).
o 4 selected references:

o 9 GO-Terms:

o 1 Instance for LIG_CID_NIM_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P53632 PAP2
574 583 TYITVSSEDDDEDGYNPYTL TP 6 Saccharomyces cerevisiae S288c
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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