LIG_CNOT1_NIM_1

CNOT1 NIM-binding site

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.

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).

Not1 (PF04054) CCR4-Not complex component, Not1 (Stochiometry: 1 : 1)