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:
The budding yeast late-G1 Cln1/2 and Ccn1-type cyclins recognize leucine- and proline-rich (LP) docking motifs on G1-specific substrates (Koivomagi,2011; Bhaduri,2011; Bhaduri,2015, Bandyopadhyay,2020). LP motif docking is conserved across fungal Cln-type cyclins (Bandyopadhyay,2020) and is highly specific, not being recognized by early-G1 Cln3 or by S- and M-phase cyclins (Bhaduri,2015; Bhaduri,2011). Mutational studies suggest that the recognition interface for LP motifs on Cln1/2 is distinct from the hydrophobic pocket (hp) described to bind other cyclin docking motifs (Bhaduri,2015). However, in the absence of a solved structure, the binding site could not be mapped conclusively. LP motif-driven multi-site substrate phosphorylation (Ord,2019) is largely independent of orientation and distance to the Cdk p-site (Bhaduri,2011, Koivomagi,2013).
Many known Cln1/2-specific Cdk1 substrates harbour LP docking motifs. The role of the motif was confirmed in Sic1, Ste5 and Ste20 by truncation/mutation studies and dedicated assays monitoring associated phenotypic outcomes (Koivomagi,2011; Bhaduri,2011). Mutation of the Ste20 motif “SLDDPIQF” revealed that no single residue is absolutely required for Cln2 binding, but mutations at the L, P or F residues led to partial phenotypes (Bhaduri,2011). At the same time, four Cln2-binding sequences (those of Sic1, Whi5, Exo84 and Ste5) contained exact matches of the core LLPP motif with no requirement for a large hydrophobic/aromatic residue in the following residue positions (Bhaduri,2011). A mutational scan using a functional readout confirmed the requirement for L and P at positions 1 and 4, and showed that hydrophobic/aromatic residues at positions 5 and 7 modulate the motif binding affinity and functional potency (Bandyopadhyay,2020), being required when the core motif is weak. With no structure available, the final motif pattern was derived from the mutation analyses and the evolutionary conservation of multiple LP motifs (Bhaduri,2011).
Pattern Probability: 0.0001070
Present in taxon: Saccharomycetaceae
Interaction Domain:
Cyclin_N (PF00134) Cyclin, N-terminal domain (Stochiometry: 1 : 1)
o See 18 Instances for DOC_CYCLIN_yCln2_LP_2
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 10 selected references:

o 7 GO-Terms:

o 18 Instances for DOC_CYCLIN_yCln2_LP_2
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P13186 KIN2
59 62 RNDQQQAPLMPPADIKQGKE TP 2 Saccharomyces cerevisiae S288c
P39969 BOI2
353 356 NNANIYNQLMPPANVDQRAS TP 2 Saccharomyces cerevisiae S288c
P39083 RGA1
329 335 ELLTSVLHSPVSVNMKNPKG TP 2 Saccharomyces cerevisiae S288c
P40095 YER158C
318 324 PEPITSLDQPVEIIKQSFST TP 2 Saccharomyces cerevisiae S288c
Q99332 FRT1
18 21 NPGSRNCTLLPPSFPRGFCK TP 2 Saccharomyces cerevisiae (Baker"s yeast)
P38283 SLI15
513 516 NYRLTNLQLLPPAEAERDDL TP 2 Saccharomyces cerevisiae S288c
P47046 IRC8
478 481 TTNRDKSKLLPPFRFTSESD TP 2 Saccharomyces cerevisiae S288c
P41832 BNI1
897 903 EFEKDRLEPPIHIKKPKVKK TP 2 Saccharomyces cerevisiae S288c
P21192 ACE2
400 406 RINGNSLRSPFLVGTDKSRD TP 2 Saccharomyces cerevisiae S288c
Q03898 FIN1
47 53 TSQKEFLKPPMRISPNKTDG TP 2 Saccharomyces cerevisiae S288c
P38261 EXO84
294 297 ESHSNSPALLPPLKAGQNGN TP 4 Saccharomyces cerevisiae S288c
P43560 LAM5
23 29 TDSVKQLGPPFEHASNNDNA TP 3 Saccharomyces cerevisiae S288c
P38634 SIC1
137 140 EEEEEGEVLLPPSRPTSARQ TP 10 Saccharomyces cerevisiae S288c
Q12416 WHI5
138 141 YDGHVSMPLLPPTTPKSRRS TP 7 Saccharomyces cerevisiae S288c
Q03497 STE20
88 94 DNNVVSLDDPIQFTRVSSSS TP 5 Saccharomyces cerevisiae S288c
P32917 STE5
278 281 SRFPPYSPLLPPFGLSYTPV TP 6 Saccharomyces cerevisiae S288c
P40091 PEA2
199 205 DIKPIPLDDPVKFLKNGINS TP 2 Saccharomyces cerevisiae S288c
P40316 PDS1
40 46 RSHSNILKPPVRLDQLKRDA TP 2 Saccharomyces cerevisiae S288c
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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