The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
Yeast Cdc14 phosphatase docking site
Functional site description:
Progression through the cell cycle is characterized by a quantitative increase in Cdk phosphorylation activity, coupled with changes in the substrate specificities of the sequentially expressed cyclin activators. This Cdk activity is modulated by opposing phosphatase activities. The conserved dual-specificity phosphatase Cdc14 is required for mitotic exit in budding yeasts. Cdc14 is released from association with its stoichiometric inhibitor Net1 during mitotic exit, allowing nuclear translocation and the sequential dephosphorylation of its targets. The non-catalytic, N-terminal domain of Cdc14 harbours a hydrophobic binding pocket that recognizes the PxL docking motif on substrates. This docking event enhances target recognition and dephosphorylation, even in the case of suboptimal phosphosites. The docking site often occurs within clusters of Cdk phosphorylation sites but also at a considerable distance from the phosphorylation site itself.
ELM Description:
The Cdc14 substrate docking PxL motif interacts with a hydrophobic groove of Cdc14. The motif ΦxxφPxLxΦ was derived from a phage display-based peptide screen of the budding yeast proteome, together with a mutational scanning peptide array of the Cbk1 protein kinase substrate and structural studies of two substrates. Cdc14-interacting peptides derived from the phage display assay harbour a PxL motif, and known interactors of Cdc14 were among the highly enriched hits, three confirmed to bind Cdc14 in vitro (Kataria,2018).
Structural and evolutionary analysis of the high-ranking phage display hits led to the formulation of the [FYLIM]xx[YVILA]PxL motif pattern, where the core PxL motif (P at +1) is accompanied by a large hydrophobic/aromatic residue in the -4 position and a second hydrophobic residue in the -1 position. The contribution of the residue in the +5 position was ambiguous based on peptide array analysis (Kataria,2018) and a variety of dissimilar residues (P, Y, H, Q, T, A) have been observed in this position among the experimental instances and their close homologues.
Structural analysis of Cdc14 interaction with two peptides derived from Cbk1 (6G84) and Sic1 (6G86) shows that they adopt similar conformations and mediate a comparable array of interactions with Cdc14. The central proline and leucine side chains of the PxL motif point into the core of the hydrophobic pocket. Three h-bonds between the peptide main chain and the Q106 and W108 side chains of Cdc14 further stabilize and position these core side chains. N-terminal to the PxL, the aliphatic residues at the −1 position (V85 in Cbk1 and A55 in Sic1) engage in hydrophobic interactions with the Cdc14 pocket, while the −4 phenylalanines stack against Cdc14 Y60. At the +5 position, Y90 in Cbk1 and P60 in Sic1 engage with Cdc14 W108. The orientation of the docking and active sites in the Cdc14 dimer indicate that dimerization might enhance the trans-dephosphorylation of substrates. The motif is so far identified only in budding yeast.
Pattern: [FYLIM]..[YVILA]P.L..
Pattern Probability: 0.0002446
Present in taxon: Fungi
Interaction Domain:
DSPn (PF14671) Dual specificity protein phosphatase, N-terminal half (Stochiometry: 1 : 1)
o See 10 Instances for DOC_CDC14_PxL_1
o Abstract
During the cell cycle, Cdk phosphorylation activity is modulated by opposing phosphatase activities. In budding yeast, Cdc14 acts as an antagonist of Cdk activity and a key regulator of late mitotic events such as chromosome segregation, spindle disassembly, and cytokinesis (Mocciaro,2010; Breitkreutz,2010). Cdc14 homologues have been identified in a wide range of organisms ranging from yeast to human. But the requirement of Cdc14 for mitotic exit is not conserved outside the budding yeast. The fission yeast Cdc14 homologue, Cdc14-like phosphatase 1 (Clp1; also known as Flp1) contributes to the control of cytokinesis, but is not required for other aspects of mitotic exit or Cdk1 inactivation. The nematode homologue, CDC-14 also plays a role in the regulation of cytokinesis. Among the three vertebrate paralogues (CDC14A, CDC14B, and CDC14C), the CDC14B appears to be the most functionally related to yeast Cdc14 and plays major roles in functions such as the G2/M DNA damage checkpoint, DNA repair and centrosome duplication, while CDC14A is involved in centrosome separation and cytokinesis, suggesting that the functions of CDC14 phosphatases have been partially rewired during eukaryotic evolution but preserve important roles in cell cycle and DNA damage regulation. In higher eukaryotes, the role of yeast Cdc14 is partly taken over by the PP1 and PP2A phosphatases (Wurzenberger,2011). The yeast dual-specificity phosphatase Cdc14 is sequestered in the nucleolus for most of the cell cycle by the nucleolar proteins Net1 and Tof2, and is only released into the nucleus and cytoplasm during anaphase (Visintin,1999; Shou,1999). In anaphase, the so called Fourteen Early Anaphase Release (FEAR) network (including Cdc5, Esp1, and Slk19), and the mitotic exit network (including the Dbf2-Mob1 complex) co-ordinately trigger the release of Cdc14 from the nucleolus (Shou,1999). Subsequently, Cdc14 performs the sequential dephosphorylation of its targets (Bouchoux,2011). Yeast Cdc14 forms a homodimer (5XW4; Kobayashi,2017). In vitro, Cdc14 strongly favours dephosphorylation of phosphoserines followed by a proline, with an additional positively charged residue downstream (SPxK/R) which, maybe not surprisingly, conforms to a Cdk consensus phosphorylation motif (Bremmer,2012). Phosphothreonines are poor Cdc14 substrates, due to a steric clash with the phosphatase active site (Bremmer,2012). The structure of the complex between Cdc14 and S-phosphorylated Swi6p peptide provides information on the catalytic mechanism of Cdc14 (5XW5). The non-catalytic, N-terminal pseudophosphatase domain (DSPn; Pfam:PF14671) of Cdc14 has a binding pocket that recognizes the PxL docking motif on its substrates (6G86; 6G85). This docking event enhances target recognition and dephosphorylation of both optimal and suboptimal targets, for example those containing phosphothreonines (Kataria,2018). A Cdc14 dimer can bind two of these motifs wherein the docking site of protomer 1 is much closer to the active site of protomer 2 than its own, implying that docking sites may regulate catalytic activity of the opposite protomer (Kataria,2018). The dimerization of Cdc14 is therefore essential for its function, facilitating the cis or trans dephosphorylation by increasing the local effective substrate concentration at both Cdc14 active sites and the dephosphorylation of sites both upstream and downstream of the PxL motif. The Cdc14-inhibitory Net1 protein not only occludes the Cdc14 active site but it also contacts the phosphatase at its non-catalytic domain A where its binding site overlaps with the PxL docking site, acting as a pseudosubstrate inhibitor (Kataria,2018).
o 10 selected references:

o 7 GO-Terms:

o 10 Instances for DOC_CDC14_PxL_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P38634 SIC1
SIC1_YEAST
52 60 STTKSFKNAPLLAPPNSNMG TP 4 Saccharomyces cerevisiae S288c
1 
P53197 CDH1
CDH1_YEAST
75 83 VSISSMASVPALNPSSTEDQ U 1 Saccharomyces cerevisiae S288c
1 
P53894 CBK1
CBK1_YEAST
82 90 NLGSGFTDVPALNYPATPPP TP 8 Saccharomyces cerevisiae S288c
1 
P53901 INN1
INN1_YEAST
158 166 DSSMAMRPIPPLPTESEYDY U 3 Saccharomyces cerevisiae S288c
1 
Q06616 YPR174C
YP174_YEAST
196 204 KGPNFYAKYPKLPQTNILRE TP 2 Saccharomyces cerevisiae S288c
1 
P38041 BOI1
BOB1_YEAST
378 386 EQILDMTEVPNLFADKDIFE TP 3 Saccharomyces cerevisiae S288c
1 
P32526 KAR9
KAR9_YEAST
504 512 KGKLILSSVPPLPYDETDET TP 6 Saccharomyces cerevisiae S288c
1 
P21192 ACE2
ACE2_YEAST
516 524 SNLAPLLNAPDLTDHQLEIK U 1 Saccharomyces cerevisiae S288c
1 
P38283 SLI15
SLI15_YEAST
668 676 NPQTIFGPIPPLHTDEIFPN U 3 Saccharomyces cerevisiae S288c
1 
P25558 BUD3
BUD3_YEAST
1208 1216 ERKEIFPTIPRLAPPASKIN U 4 Saccharomyces cerevisiae S288c
1 
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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