Carcinogenesis, Vol. 20, No. 2, 193-198,
February 1999
© 1999 Oxford University Press
Defining the substrate specificity of cdk4 kinasecyclin D1 complex
Genetics and Cancer Group, Dupont Pharmaceutical Co., Experimental Station E336/207, Wilmington, DE 19880-0336, USA
| Abstract |
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cdk4 kinasecyclin D1 complex (cdk4/D1) does not phosphorylate all of the sites within retinoblastoma protein (Rb) equally. Comparison of five phosphorylation sites within the 15 kDa C domain of Rb indicates that Ser795 is the preferred site of phosphorylation by cdk4/D1. A series of experiments has been performed to determine the properties of this site that direct preferential phosphorylation. For cdk4/D1, the preferred amino acid at the third position C-terminal to the phosphorylated serine/threonine is arginine. Substitution of other amino acids, including a conservative change to lysine, has dramatic effects on the rates of phosphorylation. This information has been used to mutate less favorable sites in Rb, converting them to sites that are now preferentially phosphorylated by cdk4/D1. A conserved site at Ser842 in the related pocket protein p107 is also preferentially phosphorylated by cdk4/D1. Although Rb and p107 differ significantly in sequence, the Rb Ser795 site can replace the p107 Ser842 site without affecting the rate of phosphorylation. These results suggest that although a determinant of specificity resides in the sequences surrounding the phosphorylated site, the structural context of the site is also a critical parameter of specificity.
Abbreviations: BSA, bovine serum albumin; cdk, cyclin-dependent kinase; cdk4/D1, cdk4 kinasecyclin D1 complex; DTT, dithiothreitol; GST, glutathione S-transferase; Rb, retinoblastoma protein.
| Introduction |
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The retinoblastoma protein (Rb) is a key regulator of cell cycle progression, through its interaction with numerous cellular proteins. Rb binds various proteins either through its A-B `pocket' domain or the C domain. This binding is controlled by the phosphorylation states of Rb: unphosphorylated and hypophosphorylated forms are associated with the active state of Rb, while hyperphosphorylated Rb represents the inactive state (for reviews see refs 13 and references therein). Phosphorylation of Rb results from the action of a number of different cyclin-dependent kinases (cdk) at various times during the cell cycle (4,5). Increasing evidence suggests that the progressive phosphorylation of Rb during the cell cycle is not a stochastic process, implying that each cdk has an inherent site specificity for phosphorylation (6,7).
The determinants for site specificity of the cdks have previously been studied using peptides as substrates (8). From these studies a consensus sequence of (S/T)PX(R/K) has been derived for the cdk4 kinasecyclin D1 complex (cdk4/D1). However, these studies measured total phosphorylation of the peptides, rather than initial rates of phosphorylation. Using initial rate measurements, we have shown profound differences in phosphorylation between the various sites within the C domain of Rb, with the preferred site being Ser795 (9). These in vitro measurements correlate with in vivo function, since it has been demonstrated that the Rb Ser795 site, one of the preferred sites for in vitro cdk4/D1 phosphorylation, is absolutely critical in vivo for inactivation of Rb growth suppression (6).
We have been interested in determining the factors that govern substrate site specificity as a tool for drug discovery. Comparison of the catalytic efficiency, Vmax/Km, of a glutathione S-transferase (GST)Rb fusion protein (amino acids 792928) with a peptide from Rb (amino acids 790802) containing the Ser795 site indicates that the peptides are phosphorylated 1000 times less efficiently by cdk4/D1 (9). These results suggest that structure plays an important role in phosphorylation efficiency of sites in the Rb C domain by cdk4/D1, either by imparting information for site specificity or by constraining the site into a more favorable conformation. In addition, sequences immediately surrounding the phosphorylation site could influence site specificity within the context of structure.
To address these possibilities we have taken three approaches. First, the C domain of the related pocket protein p107 (10) was examined for any cdk4/D1 preferential phosphorylation sites. Although Rb and p107 are related proteins, their C domains share <30% sequence identity (10). Thus, the p107 C domain was analyzed for the presence of a preferential site for cdk4/D1 phosphorylation. Second, amino acids encompassing the preferential cdk4/D1 site were mutated to determine the residues that influence site specificity. Finally, a series of phosphorylation sites were exchanged within the Rb C domain to address the issue of context on the efficiency of phosphorylation by cdk4/D1.
| Materials and methods |
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Plasmid construction
The C-terminal domain of p107 (10) was PCR amplified from HeLa cell cDNA (Clontech) using primers 5'-CTTGCTAAGGATCCGACTTGGCGAATCAGGACC-3' and 5'-GGAACTTGGAATTCTCATTAATGATTTGCTCTTTCACTGA-3'. The resulting PCR fragment containing codons 817935 was then cleaved with BamHI and EcoRI and ligated into the vector pGEX4T-1 (Pharmacia) to create a GST fusion. Site-directed mutants in this fusion construct were made using a previously described megaprimer PCR strategy (11). Plasmids containing GSTRb (codons 792928) and various mutated derivatives have been described previously (9). All constructs were verified by automated DNA sequence analysis.
Expression and purification of GSTpRb and GSTp107 constructs
GST fusion constructs were transformed into Escherichia coli strain BL21 (F ompT, rBmB) (12). For protein expression, cells were induced by addition of isopropyl-ß-D-thiogalactopyranoside (Bethesda Research Laboratories, Bethesda, MD) to 1 mM final concentration and grown for 3 h at 30°C. Purification of the GSTRb and GSTp107 fusion proteins was carried out as described previously (9). Protein concentration was determined using a Bio-Rad (Richmond, CA) protein assay with bovine serum albumin (BSA) as the standard and the purity assessed by analyzing samples by SDSPAGE and staining with Coomassie blue for protein visualization. Fusion proteins were routinely >90% pure.
Purification of cdk4/D1
Insect cell extracts expressing recombinant human cdk4/D1 were prepared as described previously (9) following dual infection by baculoviruses containing each of the kinase components. Cdk4/D1 complexes were purified to near homogeneity from these extracts by chromatography over DEAESepharose in buffer C [20 mM NaCHES, pH 9.0, 1 mM NaF, 0.5 mM Na2EDTA, 1 mM dithiothreitol (DTT), 5% glycerol] using a linear gradient of 01 M NaCl. Active fractions eluting at 250 mM NaCl were pooled, mixed with a 30-fold molar excess of GSTRb 60 kDa, which contains the A and B domains that bind cyclin, and dialyzed overnight against buffer C. The resulting GSTRb::cdk4/D1 complex was bound to a glutathioneSepharose column, washed with buffer C and the cdk4/D1 eluted with buffer C containing 1 M NaCl and a 12-fold molar excess of a 10 amino acid peptide containing the LXCXE binding motif [TDLYCYEQLN] (3). Active fractions were pooled, dialyzed overnight against 20 mM TrisHCl, pH 8.5, 1 mM NaF, 0.5 mM Na2EDTA, 1 mM DTT, 5% glycerol. Fractions were stored at 70°C in 400 µl aliquots, thawed before use and then discarded. The specific activity of the purified cdk4/D1 was 100 000 U/mg.
In vitro kinase reactions
cdk4/D1 kinase activity was measured as described previously using GSTRb fusion proteins and capturing the reaction products on glutathioneSepharose beads (13). Briefly, each reaction (300 µl) contained 50 mM TrisHCl, pH 7.6, 10 mM MgCl2, 10% DMSO, 1 mM DTT, 50 µM ATP, 6 µCi [
-32P]ATP and 180 µg GSTRb fusion protein. Reactions were initiated by addition of 25 U purified cdk4/D1. Reactions were terminated by extraction of 25 µl aliquots at the times indicated in the figures and addition to 50 µl cold phosphate-buffered saline containing 100 mM Na2EDTA, 10 mM ATP, 200 µg/ml BSA and 0.2% NP-40. Aliquots (50 µl) were then transferred to glutathioneSepharose beads and processed as described previously (13).
| Results |
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Analysis of phosphorylation of the C-terminal domain of p107
Our initial studies using baculovirus-infected cell extracts containing cdk4/D1 indicated that the Km and Vmax for the GSTRb 60 kDa fusion protein were indistinguishable from those of the GSTRb 15 kDa substrate (9). Comparison of initial velocities under conditions of excess Rb substrate indicated that cdk4/D1 had a distinct kinetic preference for the potential phosphorylation sites in the C domain of Rb. Particularly striking was the marked preference for phosphorylation at Rb Ser795. A similar experiment using purified cdk4/D1 and Rb at concentrations 15 times the Km is shown in Figure 1A
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To determine whether the above phenomenon is unique to Rb, an alternative substrate was examined for its phosphorylation by cdk4/D1. While the in vivo role of the related pocket protein p107 is not completely understood, in vitro it can serve as a substrate for cdk4/D1 (8). The C domain of p107 was cloned and expressed as a GST fusion protein. Despite the fact that p107 belongs to the Rb protein family, there is very little sequence identity (~30%) between the C domains of p107 and Rb (10). Using the sequence (Ser/Thr) Pro to identify potential cdk4/D1 phosphorylation sites, six predicted sites were found within this region of p107 (Figure 2
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Sequence determinants within the Rb Ser795 phosphorylation site
Our analogous results with p107 Ser842 and Rb Ser795 suggest that structure is a major determinant for cdk4/D1 specificity. However, the surrounding sequence could also be an important contributor. When compared with Rb Ser795, the sequence identity with p107 Ser842 appears limited to a stretch of six amino acids (Figure 2
Ser1 and Arg+2
Leu+2. The initial rate of phosphorylation of this mutant by cdk4/D1 was indistinguishable from that observed with the p107 Ser842 site (Figure 3
Lys+3, in Rb Ser795 resulted in a similar reduction in the initial rate of cdk4/D1 phosphorylation (Figure 5A
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The importance of the conserved Arg residue for cdk4/D1 phosphorylation
The results obtained thus far suggest that Arg+3 is an important modulator of cdk4/D1 phosphorylation. If we compare the other phosphorylation sites in the C domains of Rb and p107 (Figure 2
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Exchanging phosphorylation sites within the Rb C-terminal domain
While the above results certainly underscore the importance of Arg+3, it is also clear that none of the sites substituted with Arg achieves the phosphorylation rate observed with Rb Ser795. This suggests that additional residues surrounding the sites could affect the phosphorylation rate. Alternatively, the context within which the site is embedded could also exert some influence on phosphorylation. To distinguish between these possibilities a series of experiments was performed in which the phosphorylation sites within the C-terminal domain of Rb had been exchanged with one another. In the first experiment the Rb Ser807 site, ISPLK, was changed to the Rb Ser795 sequence, SSPLR. Figure 5A
| Discussion |
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Early work showed that cdks exerted control of cell cycle progression by the timing of their activity during the phases of the cell cycle (13). However, not only is the timing of phosphorylation activity of the cdks important, but each cyclin kinase has its own substrate specificity that represents an additional level of control over cell cycle progression. There have been a number of reports regarding the substrate specificity of cdk4/D1, each with differing conclusions. One analysis using full-length Rb indicated that all potential Ser/Thr Pro sites within Rb, with the exception of Ser612 and Thr821, were phosphorylated by cdk4/D1, but no attempt was made to follow the phosphorylation kinetically (15). Another study using full-length Rb indicated that Ser788 and Ser795 were the kinetically preferred sites for phosphorylation by cdk4/D1 (6). In a different report using a synthetic peptide approach, Ser780 was identified as a preferred site for phosphorylation (8). This latter study has also tested the effect of neighboring amino acids on the rate of phosphorylation by cdk4/D1. Their conclusions differ from those reported here. Namely, there appeared to be no discrimination between Lys, Arg or His at position +3. Two factors could contribute to these differences. First, the peptides, even ones containing a preferred site, are very poor substrates for cdk4/D1, differing in their catalytic efficiency from the GSTRb 15 kDa substrate by 1000-fold (8,9). Second, unconstrained peptides, as opposed to a phosphorylation site embedded in the context of a structural domain, have very different physical properties.
For the above reasons our experiments have focused on phosphorylation sites within the C domain of a truncated Rb protein which has kinetic properties and site specificity similar to the Rb protein. Our results clearly show that the amino acid at position +3 has a major role in determining the efficiency of phosphorylation by cdk4/D1. This has been demonstrated in two ways. First, mutating Arg+3 to Lys+3 in the preferred sites, p107 Ser842 or Rb Ser795, resulted in a 2-fold decrease in the initial rates of phosphorylation. In addition, changing the +3 position in non-preferred sites to Arg enhanced the initial rate of phosphorylation. Based on our analysis, Arg+3 appears to be the most favored amino acid at this position.
The data reported here support the conclusion that sequence requirements are a contributing factor in determining phosphorylation efficiency by cdk4/D1. However, the structural context of the phosphorylation site must also play an important role, one of which would be to constrain the phosphorylation site in an entropically favorable conformation. This would explain the difference observed between peptide substrates versus phosphorylation sites in the context of a protein (8,9). This would also be consistent with our phosphorylation site swapping experiments in which the sequence surrounding Ser795 was used to replace the site at Ser807. In either location the site is phosphorylated efficiently.
Merely constraining the phosphorylation site cannot be the complete explanation for the differences observed between the peptide and protein substrates. Attempts to place Ser795 in a loop on a scaffold protein failed to generate an efficiently phosphorylated site (data not shown). Furthermore, small C-terminal deletions distant from the Ser795 site abrogated phosphorylation by cdk4/D1 (9). Also, translocating the Ser795 site to Ser811 did not yield a site that was efficiently phosphorylated. In this latter experiment, the introduction of multiple mutations surrounding Ser811 could have adversely affected phosphorylation efficiency by cdk4/D1. However, this does not appear to be the case. GSTRb 15 kDa containing single phosphorylation sites at either Ser807, Ser811 or Thr821 are efficiently phosphorylated by cdc2/B and GSTRb missing all of the potential phosphorylation sites effectively inhibits phosphorylation of wild-type GSTRb (data not shown). The only poor substrate for cdkcyclin phosphorylation is Thr826, which has a Ser at position +3 instead of either Arg or Lys. The above results suggest that additional features are necessary for efficient phosphorylation. The recent X-ray structure of the Rb A and B domains, which contain two phosphorylation sites at Ser567 and Ser780, indicates that neither site is completely solvent accessible (16). Factors such as these will obviously influence the efficiency with which the site becomes phosphorylated.
Nonetheless, since (S/T)PXR is the preferred site for cdk4/D1 phosphorylation in at least two instances, Rb Ser795 and p107 Ser842, it is interesting to speculate whether other proteins are phosphorylated by cdk4/D1. A search of the database reveals >600 proteins that contain the sequence (S/T)PXR. Many of these can be eliminated as targets for cdk4/D1 since their intracellular location would make them inaccessible for phosphorylation by cdk4/D1. The remaining subset of proteins form an interesting array of cell cycle-specific proteins that warrant further study to determine whether, indeed, any of these proteins are targets for cdk4/D1 or other cdks.
| Acknowledgments |
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The authors wish to thank H.George for cdk4/D1 baculovirus-infected insect cells, the Applied Biotechnology DNA sequencing facility and M.Kendall for help in protein purification.
| Notes |
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1 To whom correspondence should be addressed Email: robert.h.grafstrom{at}dupontpharma.com
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