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, mainly through catalysing phosphorylation events. With the progression of the cell cycle, different cyclins bind to CDKs to control their function. Cyclins regulate CDK function by providing docking sites for substrates and also by modulating the active site specificity of CDKs.Docking motifs within substrates serve the precise timing of cell cycle events: they enable preferential interaction and phosphorylation of substrates by a specific cyclin/CDK complex. Certain cyclins use the conserved hydrophobic patch/pocket (hp) for the recognition of docking motifs on partner proteins. The divergence of the hp in different cyclin families has given rise to a family of related RxL-like docking motifs consisting of a hydrophobic core that can be preceded by either positively charged (RxLF or RxLxF) or hydrophobic/negatively charged residues (LxF, PxF, LP).
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}[FLMP].{0,3}[EDST]
Pattern Probability: 0.0042105
Present in taxon: Eukaryota
Interaction Domain:
Cyclin_N (PF00134) Cyclin, N-terminal domain (Stochiometry: 1 : 1)
PDB Structure: 1H28
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 cyclin-dependent kinases (CDKs) represents the periodic driving force ensuring the controlled progression of the cell cycle. Although there is functional overlap, the various cyclin/CDK complexes are clearly specialized for optimum performance of discrete tasks. However, how the specific targeting and precise timing of phosphorylation events are achieved at the molecular level still remains unclear.
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 all 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 studies revealed that much of this complexity relies on the linear encoding of SLiMs to direct cell cycle phosphorylation events (Ord,2019). Importantly, available evidence suggests that many of these mechanisms are highly conserved and have parallels in mammalian Cyclin-Cdk regulation.
Cyclins from yeasts and animals harbor a conserved surface patch called the hydrophobic pocket for the recognition of docking motifs on partner proteins, but other sites might also be used to dock substrates (DOC_CYCLIND_HELIX_1; Topacio,2019). The extensive divergence of cyclin proteins throughout evolution has led to the appearance of slightly differing hydrophobic docking pockets (hp) on their surface. As a result, cyclins that drive distinct phases of the cell cycle recognize distinct sets of RXL-like hp-binding motifs in yeasts that increase their specificity toward a set of targets with the corresponding docking motif. Budding yeast G1-CDK uses an LP (leucine- and proline-rich) substrate docking motif (DOC_CYCLIN_yLP_2; Koivomagi,2011; Bhaduri,2011) and the S-CDK an RxL docking motif (DOC_CYCLIN_RXL_1; Loog,2005) to mediate interactions with specific substrates. G2-CDK preferentially recognizes substrates with the PxF motif (DOC_CYCLIN_yPXF_4; Ord,2019). Finally, when CDK is coupled to mitotic cyclins Clb1 or Clb2, the resulting M-CDK complex recognizes the LxF motif (DOC_CYCLIN_yLXF_3; Ord,2019).
This difference in specificities can be clearly explained by changes in some of the hp residues that make up the 210-MRAILVDW-217 region of the Cyclin Box (numbering according to cyclin A) and surrounding residues (Ord,2019). The main structural information on RxL motifs comes from human Cyclin A bound to several substrates that include p53, pRb, E2F, and p107 (1H24; 1H25; 1H26; 1H28). These structures show that the positively charged R/K residue hydrogen bonds to E220, while at least two hydrophobic/aromatic positions bind in the hydrophobic pocket made up by M210, I213, L214 and W217 (Russo,1996; Lowe,2002). Residues surrounding the hydrophobic pocket (E224 and R250) shape the charge specificity of the pocket and determine a preference for basic or hydrophobic residues in the vicinity of the core motif. Loss of the acidic residue that binds the basic residue in RxL motifs (E220 in cyclin A) in yeast G1, G2 and M-type cyclins led to the evolution of related (LP, PxF and LxF) motifs that preserve the hydrophobic mode of interaction but have lower preference for RxL sequences (Bhaduri,2011; Ord,2019; Ord,2019). While the corresponding mammalian cyclin specificities are not well known, similar changes in the hp cleft make the M cyclin (Cyclin B) a poor binder of RxL motifs.
These docking motifs are not only employed by substrates, they are also frequently employed in 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).
During the course of the cell cycle there is a gradual increase in the intrinsic activity toward the optimal substrate motif. Early cyclin/CDK complexes have very low intrinsic activity compared to the intrinsically potent mitotic CDKs, still, they need to initiate such important events as Start and S phase. Results of multiple studies suggest that cyclin-specific docking sites 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 by the different cyclins combined with cyclin-specific docking site interactions reveals the dynamic nature of continuous specificity changes of Cdk1 in the course of the yeast cell cycle and provides a wide range of selective switch points for different cell cycle transitions (Koivomagi,2011). Mammalian cyclins might use similar mechanisms to ensure specific substrate docking to Cyclin/CDK complexes, but specificities different from the classical RxL motif 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
P46527 CDKN1B
27 37 HPKPSACRNLFGPVDHEELT TP 6 Homo sapiens (Human)
P38936 CDKN1A
16 26 PCGSKACRRLFGPVDSEQLS TP 5 Homo sapiens (Human)
P38634 SIC1
111 119 QEPLGRVNRILFPTQQNVDI TP 1 Saccharomyces cerevisiae S288c
P38634 SIC1
86 96 FPKSSVKRTLFQFESHDNGT TP 1 Saccharomyces cerevisiae S288c
P09119 CDC6
11 19 ITPTKRIRRNLFDDAPATPP TP 2 Saccharomyces cerevisiae (Baker"s yeast)
Q03898 FIN1
191 199 LPRAKLKGKNLLVELKKEEE TP 1 Saccharomyces cerevisiae S288c
Q13352-2 ITGB3BP
2 10 MPVKRSLKLDGLLEENSFDP TP 3 Homo sapiens (Human)
Q14207 NPAT
1059 1070 AAKPCHRRVLCFDSTTAPVA TP 2 Homo sapiens (Human)
911 920 VQEVTKVRRNLFNQELLSPS TP 1 Homo sapiens (Human)
O43303 CCP110
583 593 NSFEKVKRRLDLDIDGLQKE TP 3 Homo sapiens (Human)
Q14493 SLBP
94 103 NKEMARYKRKLLINDFGRER TP 1 Homo sapiens (Human)
P30291 WEE1
177 187 TPPHKTFRKLRLFDTPHTPK TP 2 Homo sapiens (Human)
196 207 NVTSNARRSLNFGGSTGTVP TP 3 Homo sapiens (Human)
O75179 ANKRD17
1927 1938 TWGPFPVRPLSPARATNSPK TP 3 Homo sapiens (Human)
A8T798 UL32
415 427 PPARKPSASRRLFGSSADED TP 2 Human herpesvirus 5 (Human cytomegalovirus)
P50445 rux
245 254 PTARRCVRRTLFTEENTQKE TP 1 Drosophila melanogaster (Fruit fly)
P30304 CDC25A
9 18 GPEPPHRRRLLFACSPPPAS TP 1 Homo sapiens (Human)
P06789 E1
124 134 SGQKKAKRRLFTISDSGYGC TP 4 Human papillomavirus type 18
P28749 RBL1
655 664 SPTAGSAKRRLFGEDPPKEM TP 3 Homo sapiens (Human)
Q13352 ITGB3BP
2 10 MPVKRSLKLDGLLEENSFDP TP 1 Homo sapiens (Human)
P38826 ORC6
175 186 ESPSITRRKLAFEEDEDEDE TP 1 Saccharomyces cerevisiae (Baker"s yeast)
P39880 CUX1
1298 1307 HNYRSRIRRELFIEEIQAGS TP 1 Homo sapiens (Human)
P04637 TP53
378 388 GQSTSRHKKLMFKTEGPDSD TP 4 Homo sapiens (Human)
Q08999 RBL2
677 687 PPASTTRRRLFVENDSPSDG TP 1 Homo sapiens (Human)
Q14209 E2F2
84 92 PAGRLPAKRKLDLEGIGRPV TP 1 Homo sapiens (Human)
P49918 CDKN1C
28 38 LVRTSACRSLFGPVDHEELS TP 1 Homo sapiens (Human)
O00716 E2F3
131 141 GGGPPAKRRLELGESGHQYL TP 1 Homo sapiens (Human)
Q9WTQ5 Akap12
498 507 IKVQGSPLKKLFSSSGLKKL TP 1 Mus musculus (House mouse)
Q99741 CDC6
91 99 PHSHTLKGRRLVFDNQLTIK TP 2 Homo sapiens (Human)
Q01094 E2F1
87 97 LGRPPVKRRLDLETDHQYLA TP 3 Homo sapiens (Human)
P06400 RB1
870 880 SNPPKPLKKLRFDIEGSDEA TP 3 Homo sapiens (Human)
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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