The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
CNOT1 NIM-binding site
Functional site description:
The CNOT1 (CCR4-NOT complex subunit 1) interacting motif (NIM) is conserved in the paralogous RNA-binding proteins Nanos-1, -2 and -3. Nanos proteins consist of a conserved CCHC-type zinc finger domain and variable N-terminal and C-terminal extensions. The zinc finger domain is essential for Nanos function because it mediates RNA-binding and binding to a Nanos partner (Pumilio) that mediates mRNA target specificity. Nanos proteins interact with the NOT1 superfamily homology domain (SHD) in the C-terminal part of CNOT1, thereby recruiting the CCR4-NOT deadenylase complex. The CCR4-NOT complex is a main effector complex for Nanos function and interacts with the N-terminal region of Nanos proteins. The 10-amino-acid-long NIM peptides are effectual for the recruitment of the CCR4-NOT complex to mRNA.
ELM Description:
The CNOT1-interacting motif (NIM) is present in the Nanos-1, -2 and -3 proteins and binds the C-terminal SH domain of CNOT1. The motif is present in Metazoa, but seems to be missing in several animal lineages, including TAXON:7215, where Nanos was shown to bind the CNOT4 subunit (Kadyrova,2007). The peptide adopts a partly helical conformation when bound and is largely composed of hydrophobic residues. Hence, binding mainly involves hydrophobic interactions, several of which are mediated by conserved aromatic residues. The aromatic residue in the first position, which is most often a phenylalanine, is one of the key residues of the motif and is buried in a hydrophobic pocket formed by the residues Trp2338, Phe2337 and Glu2350 of CNOT1. A second important contact is mediated by the aromatic residue in position 4, which interacts with Ile2330 of CNOT1. A third important aromatic residue is the highly conserved tyrosine in position 7, which is buried in a pocket on the CNOT1 surface formed by Met2361, Phe2353 and Gln2354. Finally, the invariant leucine in position 10 also provides hydrophobic contacts, stabilizes the peptide helix and therefore is important for the helical structure the peptide adopts upon binding. Due to the helical conformation, several positions cannot accommodate proline. In addition, proline is not allowed in the second position. Although the residue in this position is not part of the helix, it likely provides an intra-peptide hydrogen bond with the invariant aspartate in position 6, thereby stabilizing the bound structure. The crystal structure shows a 2:2 complex (4CQO), but it is unlikely that CNOT1 and Nanos form such a complex in vivo, as CNOT1 is part of the multi-subunit CCR4-NOT complex. In case of the observed 2:2 complex, binding of CNOT2 and CNOT3 to CNOT1, which is essential to form the CCR4-NOT complex, would not be possible as one of the Nanos peptides in the crystal overlaps the CNOT3-binding site on CNOT1 (4C0D) (Boland,2013).
Pattern: [FY][^P].[WFY][^P]DY..L
Pattern Probability: 5.437e-08
Present in taxon: Metazoa
Not represented in taxons: Arthropoda Lophotrochozoa Nematoda
Interaction Domain:
Not1 (PF04054) CCR4-Not complex component, Not1 (Stochiometry: 1 : 1)
o See 10 Instances for LIG_CNOT1_NIM_1
o Abstract
The CCR4-NOT complex is a multi-subunit complex that regulates gene expression. The different subunits have a very specific role in the expression of the genome (Collart,2011). This multi-protein complex controls mRNA metabolism and plays a major role in deadenylation of cytoplasmic mRNA. Deadenylase enzymes shorten the poly(A)tails of mRNAs and therefore play an important role in translational repression or mRNA degradation (Bartlam,2011). One important component of the complex is the CCR4-NOT transcription complex subunit 1 (CNOT1) (Ito,2011). CNOT1 is important for the formation of the complex, regulates the deadenylase activity and exists predominantly in the cytoplasm, where it is involved in P-body formation (Ito,2011). CNOT1 also mediates direct interactions with RNA-binding proteins, including the sequence-specific RNA-binding protein Tristetraprolin (TTP), which directly binds to adenylate-uridylate-rich elements (AREs) and controls the rapid decay of ARE-containing mRNAs. CNOT1 is also involved in specific recruitment via miRNA, because the interaction between the CCR4-NOT complex and the W-motifs in GW182 protein family members (comprising the amino acids GSTW or WGST) depends on the presence of the CNOT1 subunit (Doidge,2012).
The CNOT1-interacting motif (NIM) in the N-terminal part of Nanos-1, -2, and -3 interacts with the CCR4-NOT deadenylation complex by binding to the CNOT1 subunit, which leads to the suppression of specific mRNAs. The activity of Nanos proteins plays an essential role in germline development. Hence germline precursor cells lacking Nanos activity inappropriately express somatic genes and enter apoptosis during migration (Suzuki,2012) (Lai,2011).
o 4 selected references:

o 8 GO-Terms:

o 10 Instances for LIG_CNOT1_NIM_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P60322 Nanos2
6 15 MDLPPFDMWRDYFNLSQVVM TP 4 Mus musculus (House mouse)
Q4QRE8 nanos3
23 32 TRNQDFQPWKDYMGLADMIR TP 1 Danio rerio (Zebrafish)
M1ZML1 nanos2
17 26 TADGCFLMWRDYMDLRRTLS TP 1 Danio rerio (Zebrafish)
E7FDB3 nanos1
19 28 SYDYTFNFWNDYLGLSTLVT TP 1 Danio rerio (Zebrafish)
F6ZT24 nanos3
4 13 MSSFSIWKDYLGLNALVRQL TP 1 Xenopus (Silurana) tropicalis (Western clawed frog)
F6X9D2 Uncharacterized protein
5 14 STMEFDRWKDYFALALLVPK TP 1 Xenopus (Silurana) tropicalis (Western clawed frog)
Q90ZZ6 nanos1
7 16 DGGLCFNSWSDYLGLSSLIS TP 2 Xenopus (Silurana) tropicalis (Western clawed frog)
P60323 NANOS3
4 13 MGTFDLWTDYLGLAHLVRAL TP 3 Homo sapiens (Human)
P60321 NANOS2
6 15 MQLPPFDMWKDYFNLSQVVW TP 3 Homo sapiens (Human)
40 49 AHPQPFSSWNDYLGLATLIT TP 4 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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