The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Cyclin N-terminal Domain Docking Motifs
Functional site description:
Cyclin-dependent kinases (Cdks) coordinate hundreds of molecular events during the cell cycle via Ser/Thr phosphorylation. With cell cycle progression, different cyclins bind to Cdks to control their function by providing docking sites for substrates and also by modulating Cdk active site specificity. Docking motifs control the timing of cell cycle events by enabling preferential interaction and phosphorylation of substrates by a specific cyclin/Cdk complex. Cyclins use the conserved hydrophobic pocket (hp) to bind docking motifs on partner proteins. In the budding yeast, the divergence of the hp has given rise to a family of related RxL-like docking motifs consisting of a hydrophobic core modulated by positively charged (RxLF, RxLxF) or hydrophobic (LxF, PxF, NLxxxL) residues. Cyclins may use additional surfaces to dock substrates, as with the mammalian Cyclin D-specific (DOC_CYCLIN_D_Helix_1) and the budding yeast Cln2-specific leucine- and proline-rich LP (DOC_CYCLIN_yCln2_LP_2) motifs.
ELMs with same func. site: DOC_CYCLIN_RxL_1  DOC_CYCLIN_yClb1_LxF_4  DOC_CYCLIN_yClb3_PxF_3  DOC_CYCLIN_yClb5_NLxxxL_5  DOC_CYCLIN_yCln2_LP_2 
ELM Description:
When yeast Cdk1 is coupled to mitotic cyclins Clb1 or Clb2, the resulting M-Cdk complex recognizes the LxF motif (Ord,2019) that is not recognized by other yeast cyclin-Cdk complexes (Ord,2019; Ord,2020). The preference of M-Cdk for LxF over RxL motifs can be understood based on the corresponding changes in the hydrophobic pocket of M cyclins. The E220 position (Cyclin A) that hydrogen bonds to R in the RxL motif is mutated to a positively charged K residue, and additional mutations in the alpha 1 helix (E224 for K) decrease the preference for positive charge at the motif N terminus. Mapping in the vicinity of the LxF motif with single alanine mutations confirmed the importance of the L and F amino acids and their spacing (Ord,2020) with a minor contribution of P in position −3, E in position −2, and K in the −1 position, counting from Leu in the LxF motif as +1 (Ord,2019). The conservation patterns of validated interactors also confirmed that none of the positions preceding or following the LxF motif are strictly conserved, but the preceding three positions show some preferences for P in position −3, E/N in position −2 and K/R in position −1 (Ord,2019). Additionally, a hydrophobic residue in position +4 is enriched when N-terminal positions are not optimal, with a preference for Y, F and V, which would strengthen the interaction with the core of the hydrophobic pocket. The presence of two or more of these features is likely to provide increasing binding specificity. The preferences at two positions: -3/-1, -2/-1 or -2/+4 need be satisfied to gain a high-confidence motif pattern.
The LxF-mediated interaction is not only responsible for the targeting of M-Cdk to mitotic phosphorylation substrates. It also contributes to the inhibition of M-Cdk by the replication factor Cdc6 (P09119) that is important in mitotic exit, and to the regulation of M-Cdk by Swe1 (P32944) that keeps M-Cdk in an inactive state during earlier phases of the cell cycle (Ord,2019).
Pattern: (P.[KR]L.F)|(.N[KR]L.F)|(.N.L.F[LMIVFY])
Pattern Probability: 0.0000215
Present in taxon: Fungi
Interaction Domain:
Cyclin_N (PF00134) Cyclin, N-terminal domain (Stochiometry: 1 : 1)
o See 13 Instances for DOC_CYCLIN_yClb1_LxF_4
o Abstract
Cyclin-dependent kinases (Cdks) are central regulatory enzymes of the eukaryotic cell cycle. The sequential attachment of different cyclins to Cdks represents the periodic driving force that ensures a controlled progression through the cell cycle. Although there can be functional overlap, the various cyclin/Cdk complexes are specialized for optimum performance of discrete tasks.

The cell cycle of the budding yeast Saccharomyces cerevisiae is remarkably simplified compared to that of mammalian cells and therefore it was the subject of many cell-cycle related studies and is currently better understood. Here a single Cdk, Cdk1, associates with different cyclins to mediate all major cell cycle transitions. Cyclins Cln1–3 are triggers for G1 and G1/S, while among B-type cyclins Clb5 and Clb6 drive S phase, Clb3 and Clb4 are specific for early mitotic events, and Clb1 and Clb2 complete the progression to mitosis. Detailed analyses of the budding yeast cell cycle provide important clues on the mechanisms that allow the fine-tuning of thresholds and the ordering of the switch points that drive cell cycle events. These mechanisms rely strongly on the linear encoding of SLiMs to direct cell cycle phosphorylation events (Ord,2019). Limited evidence suggests that these mechanisms have parallels in mammalian cyclin-Cdk regulation.

Cyclins from yeasts and animals harbour a highly conserved surface patch called the hydrophobic pocket (hp) that recognizes docking motifs on partner proteins (DOC_CYCLIN_RxL_1; Loog,2005). The RxL docking motif mediates binding to the hp of a broad range of cyclins from budding yeast (Clb1-6) and mammalian cells (cyclins D/E/A/B). Studies in budding yeast have identified more specific motifs that target the hp. For example, G2 cyclin Clb3 recognizes substrates with the PxF motif (DOC_CYCLIN_yClb3_PxF_3; Ord,2020), and when Cdk is coupled to mitotic cyclins Clb1 or Clb2, the resulting M-Cdk complex recognizes the LxF motif (DOC_CYCLIN_yClb1_LxF_4; Ord,2019). Likewise, the NLxxxL motif is homologous to RxL, but has evolved exclusive specificity for S-phase cyclins Clb 5/6 (DOC_CYCLIN_yClb5_NLxxxL_5; Faustova,2021). Other cyclin-specific motifs include the leucine- and proline-rich LP docking motif (DOC_CYCLIN_yCln2_LP_2; Koivomagi,2011; Bhaduri,2011), which directs binding to late G1-cyclins Cln1/2. Specific docking motifs are also present in mammalian cyclins, as with the cyclin D-specific helical docking motif (DOC_CYCLIN_D_helix_1; Topacio,2019) that mediates binding of Rb proteins to Cyclin D to drive the G1/S transition. Cyclin docking motifs are not only employed by substrates, they are also frequently employed by regulators of cyclin/Cdk complexes, for example the mammalian p27Kip1 and p21Cip1 cyclin inhibitors (1JSU; 6P8E, 6P8H) which hide the site from substrates or the yeast Swe1 that keeps M-CDK in an inactive state during earlier phases of the cell cycle (Ord,2019).

The differences in specificity of hp-docking motifs are explained by changes in the residues that make up the 210-MRAILVDW-217 helix in the hydrophobic pocket (numbering according to human cyclin A2) (Ord,2019). The structures of several RxL motifs (p53, pRb, E2F, and p107) bound to cyclin A2 (1H24; 1H25; 1H26; 1H28) reveal that the central R/K residue of the RxL motif hydrogen bonds to E220 in cyclin A2, while two hydrophobic/aromatic positions bind to an apolar groove made up by M210, I213, L214 and W217 (Russo,1996; Lowe,2002). Residues surrounding the hp (E224 and R250) shape its charge specificity and determine a preference for basic or hydrophobic residues in the vicinity of the core motif. In the budding yeast, loss of the acidic E220 residue in G2- and M-phase cyclins weakens their preference for RxL sequences, favouring the emergence of related (PxF and LxF) motifs that preserve the hydrophobic mode of interaction (Bhaduri,2011; Ord,2019; Ord,2020). Similar changes in the hydrophobic pocket of mammalian cyclins make M-cyclin (Cyclin B) a poor binder of RxL motifs.

Early cyclin/Cdk complexes have low intrinsic activity toward the optimal substrate motif compared to the potent mitotic Cdks, still they need to initiate such important events as Start and S phase. The cyclin-specific docking sites described above are able to compensate for the gradually decreasing specificity of early cyclin/Cdk complexes (Loog,2005; Koivomagi,2011; Bhaduri,2011; Bhaduri,2015; Ord,2019; Ord,2019). Also, cyclins are not just activators of Cdk1 but are also modulators of the catalytic specificity of the kinase active site (Koivomagi,2011). Therefore, modulation of Cdk1 active-site substrate specificity combined with cyclin-specific docking enables regulated changes in Cdk1 specificity and provides a wide range of selective switch points that drive cell cycle transitions (Koivomagi,2011). Mammalian cyclins might use similar mechanisms to ensure specific substrate docking at different stages of the cell cycle, but hp-docking motifs different from the canonical RxL sequence remain to be elucidated.
o 9 selected references:

o 7 GO-Terms:

o 13 Instances for DOC_CYCLIN_yClb1_LxF_4
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P32785 FMT1
9 14 VKMRRITPTRLLFTCRYISN TP 1 Saccharomyces cerevisiae S288c
P50105 TAF4
181 187 TNNVKIPNHLPFLHPEQVSN TP 1 Saccharomyces cerevisiae S288c
P24279 MCM3
152 157 SAVSSRHPWKLSFKGSFGAH FP 1 Saccharomyces cerevisiae S288c
Q03898 FIN1
118 123 NIIFPTSPTKLTFSNENKIG TP 1 Saccharomyces cerevisiae S288c
P36094 SPC42
226 231 LNTILPINNRLNFQEPKRYN TP 1 Saccharomyces cerevisiae S288c
Q06412 TUS1
136 141 SQSRERSPNKLSFIGNSEER TP 1 Saccharomyces cerevisiae S288c
P07866 LTE1
594 599 SRTDENGPQRLLFHETDKTN TP 1 Saccharomyces cerevisiae S288c
Q04116 YHP1
330 335 IKSPKGKENRLKFNAYERKP TP 1 Saccharomyces cerevisiae S288c
P41832 BNI1
1947 1952 RARKERSIGEASTGNRLSFK TP 3 Saccharomyces cerevisiae S288c
P25558 BUD3
1630 1635 EDEDGKQNCAVGGPEKLKFY TP 2 Saccharomyces cerevisiae S288c
P32944 SWE1
47 52 AIGGSTPTNKLKFYPYSNNK TP 3 Saccharomyces cerevisiae S288c
P17123 SPO12
147 152 GKKKKVNPMKLNFKGNLAAD TP 3 Saccharomyces cerevisiae S288c
P09119 CDC6
44 49 DVTPESSPEKLQFGSQSIFL TP 4 Saccharomyces cerevisiae (Baker"s yeast)
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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