The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Nrd1 CID domain ligand
Functional site description:
Noncoding RNAs are targeted by the Nrd1-Nab3-Sen1 (NNS) complex for exosome-dependent degradation. Within the NNS complex Sen1 employs three Nrd1-interacting motifs (NIMs) to bind to the CTD-interacting domain (CID) of Nrd1. The Trf4-Air2-Mtr4 (TRAMP) complex recognizes and polyadenylates the RNAs targeted by the NNS complex for degradation or processing in the exosome. It is formed by a poly(A) polymerase, Trf4 or Trf5, an RNA helicase Mtr4, and an RNA-binding zinc knuckle protein, Air1/2. The Trf4 subunit similarly binds to the CID of Nrd1 by a NIM and thereby stimulates the polyadenylation activity of the TRAMP complex. Besides Trf4, another nuclear exosome cofactor, Mpp6 also interacts with Nrd1 CID through a NIM in a competitive manner.
ELM Description:
Based on the known NIM instances, their conservation and structural considerations, NIMs are centred around a strictly conserved Tyr residue that is preceded by some negative charges, especially in the Y-2 position where only Asp, or occasionally Asn, is accepted. The Y-1 position also seems to be restricted to acidic and small residues, while the Y+2 position can only take Pro or Leu (according to mutational studies Ala and Val also (Zhang,2019), but those are not seen in alignments).

Similar to the CTD, the residues in the Y+1 to Y+4 positions of NIMs form a β turn when binding to Nrd1 CID. The conserved Y and P/L residues dock into a hydrophobic pocket of CID. The Y also interacts with the P in the Y+2 position via intramolecular stacking and forms an H-bond with the conserved D70 of Nrd1. There are a variable number of acidic residues in the six positions preceding the Y, which bind to a basic patch of CID.

Based on the sequences and binding affinities of the instances, it seems that those with Pro in the Y+2 position and/or more acidic residues N-terminal to the Y bind stronger than others (Zhang,2019). Based on the structures of the 3 Sen1 NIMs (6O3W; 6O3X; 6O3Y), accommodating the bulkier Leu at the Y+2 position slightly changes the backbone structure of the motif. In these structures, acidic positions upstream to Y-2 are disordered, contacts with CID were not seen (Zhang,2019). In the Trf4 NIM-Nrd1 CID NMR structure (2MOW), Asp residues in the Y-2 and Y-4 positions contact S25 and R28 of Nrd1, while Glu in the Y-3 and Asp in the Y-6 positions form salt bridges with K30 and K21 of Nrd1 CID, respectively.

Interestingly, the NIM motif is remarkably poorly conserved among yeast species compared to other SLiMs. The interaction might have appeared relatively recently in evolution, might be old but got lost in many yeast species, or, if the interaction is found in other species, the motif sequence might evolve very fast, even by the standards of linear motifs.
Pattern: [ED].{0,3}[DN][DEGPA]Y.[PL]..
Pattern Probability: 0.0000422
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 5 Instances for LIG_Nrd1CID_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 (Vanacova,2005). 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).
In yeasts, Nrd1-interacting motif (NIM)-mediated competitive interactions of Sen1 (Q00416), the TRAMP complex subunit Trf4 (P53632) and Mpp6 (P53725) with Nrd1 CID domain largely determine the function of these complexes (Zhang,2019; Kim,2016; Chaves-Arquero,2023). Within the NNS complex Sen1 interacts with Nrd1 with high affinity through 3 copies of NIMs (Zhang,2019): this multivalent setting also suggests that they form phase-separated condensates by liquid-liquid phase separation (LLPS). The nuclear exosome cofactors Mpp6 and Trf4 can also bind to the Nrd1 CID in a mutually exclusive manner, bridging Nrd1 and/or Nrd1-terminated transcripts to the exosome (Kim,2016). NIMs are similar to phosphorylated repeats of the RNAP II CTD (2LO6), but the binding affinity of the individual NIM motif instances to the CID domain is ~100-fold stronger (Tudek,2014; Zhang,2019; Kim,2016).
o 8 selected references:

o 9 GO-Terms:

o 5 Instances for LIG_Nrd1CID_NIM_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P53632 PAP2
575 583 TYITVSSEDDDEDGYNPYTL TP 9 Saccharomyces cerevisiae S288c
P53725 MPP6
155 162 GSQDDGEDEYDLDKLFKDSI TP 7 Saccharomyces cerevisiae S288c
Q00416 SEN1
2181 2190 DSYPAEAEDPYDLNPHPQPQ TP 5 Saccharomyces cerevisiae S288c
Q00416 SEN1
1884 1891 PVPSEQEDDYKLPMEYITQG TP 4 Saccharomyces cerevisiae S288c
Q00416 SEN1
2055 2062 NEDDDDEDDYTPSISDSSLM TP 7 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