The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
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 classical RxL cyclin recognition motif is found in a wide range of cyclin/CDK interacting proteins (Wohlschlegel,2001; Schulman,1998) including phosphorylation targets like p53, pRb, E2F, p107 (1H24; 1H25; 1H26; 1H28), and CIP-KIP family Cdk inhibitors (1JSU; 6P8E; 6P8H; Russo,1996; Wohlschlegel,2001; Guiley,2019). The presence of this docking motif substantially increases the level of phosphorylation of Cdk substrates at ([ST])Px(0,2)[KR] motifs (MOD_CDK_SPxK_1; Takeda,2001). It is highly conserved in eukaryotes. Several yeast Clb5 substrates employ RxLs for docking as do those of mammalian Cyclin A (Loog,2005; Koivomagi,2011). Cyclins show cross-specificity, for instance Cyclins E and D also bind RxL motifs (Guiley,2019).
The classical cyclin docking motif pattern is mainly derived from peptides bound to Cyclin A as there are several complex structures available. Although the motif is often called RxL, there are actually four core binding residues, with only the Leucine being fully conserved. The motif binds in a hydrophobic groove with charged residues lining the edge. Peptide backbone hydrogen bonds guide the four core binding residues into the groove. There is a clear but non-essential preference for basic residues preceding the core motif and for acidic residues following the core motif. The first core binding position is quite shallow, accepting either hydrophobic or basic residues. It is followed by a residue facing outwards, which cannot accept the short acidic residue Asp. The next residue lies in a pocket and must be either Arg or Lys. It is followed by a residue facing outwards, which cannot accept the short acidic residue Asp. Then comes the Leu residue fitting into the hydrophobic groove. Flexible spacing then allows one optional externally facing residue. The final core hydrophobic residue is one of Phe, Pro, Leu or Met. The derived regular expression pattern captures the core motif and approximates the weaker charge preference to either side.
Pattern: (.|([KRH].{0,3}))[^EDWNSG][^D][RK][^D]L.{0,1}[FL].{0,3}[EDST]
Pattern Probability: 0.0018793
Present in taxon: Eukaryota
Interaction Domain:
Cyclin_N (PF00134) Cyclin, N-terminal domain (Stochiometry: 1 : 1)
PDB Structure: 1H26
o See 31 Instances for DOC_CYCLIN_RxL_1
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 17 selected references:

o 17 GO-Terms:

o 31 Instances for DOC_CYCLIN_RxL_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
O75179-6 ANKRD17
ANR17_HUMAN
1742 1750 SPSSPSVRRQLFVTVVKTSN TP 3 Homo sapiens (Human)
P46527 CDKN1B
CDN1B_HUMAN
27 37 HPKPSACRNLFGPVDHEELT TP 6 Homo sapiens (Human)
1 
P38936 CDKN1A
CDN1A_HUMAN
16 26 PCGSKACRRLFGPVDSEQLS TP 5 Homo sapiens (Human)
1 
P38634 SIC1
SIC1_YEAST
111 119 QEPLGRVNRILFPTQQNVDI TP 1 Saccharomyces cerevisiae S288c
1 
P38634 SIC1
SIC1_YEAST
86 96 FPKSSVKRTLFQFESHDNGT TP 1 Saccharomyces cerevisiae S288c
1 
P09119 CDC6
CDC6_YEAST
11 19 ITPTKRIRRNLFDDAPATPP TP 2 Saccharomyces cerevisiae (Baker"s yeast)
1 
Q03898 FIN1
FIN1_YEAST
191 199 LPRAKLKGKNLLVELKKEEE TP 1 Saccharomyces cerevisiae S288c
Q13352-2 ITGB3BP
CENPR_HUMAN
2 10 MPVKRSLKLDGLLEENSFDP TP 3 Homo sapiens (Human)
Q14207 NPAT
NPAT_HUMAN
1059 1070 AAKPCHRRVLCFDSTTAPVA TP 2 Homo sapiens (Human)
Q7Z2Z1 TICRR
TICRR_HUMAN
911 920 VQEVTKVRRNLFNQELLSPS TP 1 Homo sapiens (Human)
O43303 CCP110
CP110_HUMAN
583 593 NSFEKVKRRLDLDIDGLQKE TP 3 Homo sapiens (Human)
Q14493 SLBP
SLBP_HUMAN
94 103 NKEMARYKRKLLINDFGRER TP 1 Homo sapiens (Human)
P30291 WEE1
WEE1_HUMAN
177 187 TPPHKTFRKLRLFDTPHTPK TP 2 Homo sapiens (Human)
Q9BY12 SCAPER
SCAPE_HUMAN
196 207 NVTSNARRSLNFGGSTGTVP TP 3 Homo sapiens (Human)
A8T798 UL32
A8T798_HCMV
415 427 PPARKPSASRRLFGSSADED TP 2 Human herpesvirus 5 (Human cytomegalovirus)
P50445 rux
RUX_DROME
245 254 PTARRCVRRTLFTEENTQKE TP 1 Drosophila melanogaster (Fruit fly)
P30304 CDC25A
MPIP1_HUMAN
9 18 GPEPPHRRRLLFACSPPPAS TP 1 Homo sapiens (Human)
P06789 E1
VE1_HPV18
124 134 SGQKKAKRRLFTISDSGYGC TP 4 Human papillomavirus type 18
1 
P28749 RBL1
RBL1_HUMAN
655 664 SPTAGSAKRRLFGEDPPKEM TP 3 Homo sapiens (Human)
Q13352 ITGB3BP
CENPR_HUMAN
2 10 MPVKRSLKLDGLLEENSFDP TP 1 Homo sapiens (Human)
P38826 ORC6
ORC6_YEAST
175 186 ESPSITRRKLAFEEDEDEDE TP 1 Saccharomyces cerevisiae (Baker"s yeast)
P39880 CUX1
CUX1_HUMAN
1298 1307 HNYRSRIRRELFIEEIQAGS TP 1 Homo sapiens (Human)
P04637 TP53
P53_HUMAN
378 388 GQSTSRHKKLMFKTEGPDSD TP 4 Homo sapiens (Human)
Q08999 RBL2
RBL2_HUMAN
677 687 PPASTTRRRLFVENDSPSDG TP 1 Homo sapiens (Human)
Q14209 E2F2
E2F2_HUMAN
84 92 PAGRLPAKRKLDLEGIGRPV TP 1 Homo sapiens (Human)
P49918 CDKN1C
CDN1C_HUMAN
28 38 LVRTSACRSLFGPVDHEELS TP 1 Homo sapiens (Human)
O00716 E2F3
E2F3_HUMAN
131 141 GGGPPAKRRLELGESGHQYL TP 1 Homo sapiens (Human)
Q9WTQ5 Akap12
AKA12_MOUSE
498 507 IKVQGSPLKKLFSSSGLKKL TP 1 Mus musculus (House mouse)
Q99741 CDC6
CDC6_HUMAN
91 99 PHSHTLKGRRLVFDNQLTIK TP 2 Homo sapiens (Human)
Q01094 E2F1
E2F1_HUMAN
87 97 LGRPPVKRRLDLETDHQYLA TP 3 Homo sapiens (Human)
P06400 RB1
RB_HUMAN
870 880 SNPPKPLKKLRFDIEGSDEA TP 3 Homo sapiens (Human)
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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