Opposite and mutually incompatible structural requirements of type-2 casein kinase and cAMP-dependent protein kinase as visualized with synthetic peptide substrates

Substrate specificity of the herpes simplex virus type 2 UL13 protein kinase

The UL13 protein kinase is conserved among many herpesviruses but HSV-2 UL13 specificity is not known. Here, we found that HSV-2 UL13 is a phosphoprotein that autophosphorylates, and that serines within ERK and Cdc2 motifs were important for autophosphorylation but not for UL13 phosphorylation of exogenous substrates. HSV-2 UL13 phosphorylated a peptide also recognized by ERK and Cdc2. However, mutation of substrate residues critical for Cdc2 or Erk phosphorylation did not alter HSV-2 UL13 phosphorylation of the peptide, and HSV-2 UL13 did not phosphorylate standard Cdc2 or Erk peptide substrates. Mutation of prolines surrounding the peptide phosphoacceptor site reduced phosphorylation by HSV-2 UL13, and a peptide containing serine-proline amid alanines and glycines was phosphorylated. Thus, HSV-2 UL13 does not mimic ERK or Cdc2 substrate recognition and its minimal recognition motif can be serine-proline. This motif's simplicity indicates that distal sequence or protein structure contributes to HSV-2 UL13 substrate specificity.

Dephosphorylation of phosphopeptides by calcineurin (protein phosphatase 2B)

38 (6-32 residues) enzymically phosphorylated synthetic peptides have been assayed as substrates for calcineurin, a Ca2+/calmodulin-dependent protein phosphatase (PP-2B) belonging to the family of Ser/Thr-specific enzymes but also active on phosphotyrosine residues. Many peptides reproduce, with suitable modifications, naturally occurring phosphoacceptor sites. While protein phosphatases 2A and 2C are also very active on short phosphopeptides, an extended N-terminal stretch appears to be a necessary, albeit not sufficient, condition for an optimal dephosphorylation, comparable to that of protein substrates, of both phosphoseryl and phosphotyrosyl peptides by calcineurin. This finding corroborates the view that higher-order structure is an important determinant for the substrate specificity of calcineurin. However, a number of shorter peptides are also appreciably dephosphorylated by this enzyme, their efficiency as substrates depending on local structural features. All the peptides that are appreciably dephosphorylated by calcineurin contain basic residue(s) on the N-terminal side. A basic residue located at position -3 relative to the phosphorylated residue plays a particularly relevant positive role in determining the dephosphorylation of short phosphopeptides. Acidic residue(s) adjacent to the C-terminal side of the phosphoamino acid are conversely powerful negative determinants, preventing the dephosphorylation of otherwise suitable peptide substrates. However, calcineurin displays an only moderate preference for phosphothreonyl peptides which are conversely strikingly preferred over their phosphoseryl counterparts by the other classes of Ser/Thr-specific protein phosphatases. Moreover calcineurin does not perceive as a strong negative determinant the motif Ser/Thr-Pro in peptides where this motif prevents dephosphorylation by the other classes of Ser/Thr protein phosphatases. Whenever tested on phosphotyrosyl peptides, calcineurin exhibits a specificity which is strikingly different from that of T-cell protein tyrosine phosphatase, a bona fide protein tyrosine phosphatase. In particular while the latter enzyme is especially active toward a number of phosphopeptides reproducing the phosphoacceptor sites of src products and of calmodulin whose N-terminal moieties are predominantly acidic, the artificial substrate phospho-angiotensin II, bearing an arginine residue at position -2, is far preferred by calcineurin over all phosphotyrosyl peptides of similar size. Collectively taken these results show that the specificity of calcineurin, rather than resting on a given consensus sequence, is determined by a variety of primary and higher-order structural features conferring to it an overall selectivity that is different from those of any other known protein phosphatase.

Specificity of T-cell protein tyrosine phosphatase toward phosphorylated synthetic peptides

The local specificity determinants for a T-cell protein tyrosine phosphatase (TC-PTP) have been inspected with the aid of a series of synthetic peptides, either enzymically or chemically phosphorylated, derived from the phosphoacceptor sites of phosphotyrosyl proteins. The truncated form of T-cell PTP, deprived of its C-terminal down-regulatory domain, readily dephosphorylates submicromolar concentrations of eptapeptides to eicosapeptides, reproducing the C-terminal down-regulatory site of pp60c-src (Tyr527), the phosphorylated loop IV of calmodulin and the main autophosphorylation site of two protein tyrosine kinases of the src family (Tyr416 of pp60c-src and Tyr412 of p51fgr). However, phosphopeptides of similar size, derived from phosphoacceptor tyrosyl sites of the abl and epidermal-growth-factor receptor protein tyrosine kinases, the phosphorylated loop III of calmodulin, and phosphoangiotensin II undergo either very slow or undetectable dephosphorylation, even if tested up to 1 microM concentration. The replacement of either Ser-P or O-methylated phosphotyrosine for phosphotyrosine within suitable peptide substrates gives rise to totally inert derivatives. Moreover, amino acid substitutions around phosphotyrosine in the peptides src(412-418), src(414-418) and abl-(390-397) deeply influence the dephosphorylation efficiency. From these data and from a comparative analysis of efficient versus poor phosphopeptide substrates, it can be concluded that acidic residues located on the N-terminal side of phosphotyrosine, with special reference to position -3, play a crucial role in substrate recognition, while basic residues in the same positions act as negative determinants. In any event, the presence of at least two aminoacyl residues upstream of phosphotyrosine represents a necessary, albeit not sufficient, condition for detectable dephosphorylation to occur. By replacing the truncated form of TC-PTP with the full length TC-PTP, the dephosphorylation efficiencies of all peptides tested are dramatically impaired. Such an effect is invariably accounted for by a substantial increase in Km values, accompanied by a more or less pronounced decrease in Vmax values. These data support the concept that the C-terminal regulatory domain of TC-PTP exerts its function primarily by altering the affinity of the enzyme toward its phosphotyrosyl targets.

Purification of a soluble casein kinase II from Dictyostelium discoideum lacking the beta subunit: regulation during proliferation and differentiation

A type II casein kinase has been purified from the soluble fraction of Dictyostelium discoideum vegetative cells. The enzyme has been purified 370 fold and behaves catalytically as casein kinase type II, in the sense that it utilizes GTP as well as ATP as phosphoryl donors, it is inhibited by low heparin concentrations and phosphorylates a specific peptide for CK II. It is a tetramer of 38 kDa-subunits with catalytic activity and ability to autophosphorylate in vitro. The comparison of this activity with the nuclear enzyme previously purified from the same organism indicates that both have the same molecular structure. Both enzymes have antigenic determinants in common with casein kinase II from bovine thymus, suggesting a high degree of conservation during evolution. Studies on the activity of this enzyme during early differentiation, and in the transition from quiescence to proliferation shows an increase in specific activity suggesting a crucial role for the enzyme in this organism.

The comparative efficiencies of the Ser(P)-, Thr(P)- and Tyr(P)-residues as specificity determinants for casein kinase-1

The beta-casein derived phosphopeptide, Glu-Glu-Ser(P)-Glu-Glu-Ser-Ile-Thr-NHMe and two derivatives in which the Ser(P)-residue is replaced by the Thr(P)- and Tyr(P)-residue have been compared for their susceptibility to phosphorylation by casein kinase-1. While both the Ser(P)- and Thr(P)-peptides are good substrates with similar kinetic constants, the Tyr(P)-peptide is a substrate as poor as the unphosphorylated derivative EEEEESIT, exhibiting a 21-fold higher Km and 6-fold lower Vmax values. While prior dephosphorylation of the Ser(P)-peptide caused a marked loss in its phosphoacceptor capacity, prior dephosphorylation of the Tyr(P)-peptide caused no significant change in its poor phosphoacceptor capacity. Thus the order of efficiency of phosphoaminoacids as specificity determinants for casein kinase-1 was found to be Ser(P)=Thr(P) much greater than Tyr(P) and this order is markedly different from Tyr(P) greater than Ser(P) much greater than Thr(P) which was previously established for casein kinase-2 [Meggio et al. (1991) FEBS Lett. 279, 307-309].

Isolation and characterization of recombinant human casein kinase II subunits alpha and beta from bacteria

cDNA encoding the casein kinase II (CKII) subunits alpha and beta of human origin were expressed in Escherichia coli using expression vector pT7-7. Significant expression was obtained with E. coli BL21(DE3). The CKII subunits accounted for approximately 30% of the bacterial protein; however, most of the expressed proteins were produced in an insoluble form. The recombinant CKII alpha subunit was purified by DEAE-cellulose chromatography, followed by phosphocellulose and heparin-agarose chromatography. The recombinant CKII beta subunit was extracted from the insoluble pellet and purified in a single step on phosphocellulose. From 10 g bacterial cells, the yield of soluble protein was 12 mg alpha subunit and 5 mg beta subunit. SDS/PAGE analysis of the purified recombinant proteins indicated molecular masses of 42 kDa and 26 kDa for the alpha and beta subunits, respectively, in agreement with the molecular masses determined for the subunits of the native enzyme. The recombinant alpha subunit exhibited protein kinase activity which was greatest in the absence of monovalent ions. With increasing amounts of salt, alpha subunit kinase activity declined rapidly. Addition of the beta subunit led to maximum stimulation at a 1:1 ratio of both subunits. Using a synthetic peptide (RRRDDDSDDD) as a substrate, the maximum protein kinase stimulation observed was fourfold under the conditions used. The Km of the reconstituted enzyme for the synthetic peptide (80 microM) was comparable to the mammalian enzyme (40-60 microM), whereas the alpha subunit alone had a Km of 240 microM. After sucrose density gradient analysis, the reconstituted holoenzyme sedimented at the same position as the mammalian CKII holoenzyme.

Mouse ornithine decarboxylase is phosphorylated by casein kinase-II at a predominant single location (serine 303)

Ornithine decarboxylase (ODC), a key enzyme in the biosynthetic pathway of polyamines in mammalian cells is characterized by an extremely short half-life and by a rapid induction following stimulation with growth-promoting agents. Inspection of its deduced amino acid sequence revealed the presence of sequences that may serve as targets for phosphorylation by casein kinase II (CK-II). In the present study we demonstrate that ODC serves as a substrate for phosphorylation by CK-II in vitro and that it is phosphorylated in intact mammalian cells. One-dimensional phosphopeptide analysis demonstrated that all the phosphopeptides generated by V8 protease digestion of in vivo phosphorylated ODC correspond to the major phosphopeptides of ODC phosphorylated in vitro by CK-II. Phosphopeptide analysis of wild-type ODC and of a mutant in which serine 303 was converted to alanine demonstrated that the latter lacks the phosphopeptides that correspond to those detected in ODC phosphorylated in vivo. In addition, no incorporation of phosphate into the alanine 303 mutant was observed when it was expressed in transfected cos cells. Based on these observations, we conclude that in mammalian cells serine 303 is the major (if not the only) phosphorylated residue of ODC and that CK-II or another cellular kinase with very similar sequence specificity is responsible for manifestation of this modification. The unphosphorylated alanine 303 mutant retained enzymatic activity, which decayed at a similar rate to that of the wild-type enzyme. We therefore conclude that phosphorylation is not essential for maintaining enzymatic activity or regulating ODC turnover.

Phosphoserine in peptide substrates can specify casein kinase II action

Casein kinase II is a ubiquitous serine/threonine protein kinase which utilizes acidic amino acid residues as recognition determinants in its substrates, the motif -S/T-X-X-D/E- being particularly important. To test whether a phosphoserine residue can act as a substrate determinant, a peptide was synthesized, containing the sequence -S-X-X-S, which was not phosphorylated by casein kinase II. However, upon phosphorylation at the +3 position, the peptide became a substrate for casein kinase II. With another peptide, a positive influence of more distal phosphorylations was found. The results indicate the potential for casein kinase II to participate in hierarchal phosphorylation schemes.

Investigation of the substrate specificity of thylakoid protein kinase using synthetic peptides

Synthetic peptide analogues of the N-terminal region of the light harvesting chlorophyll a/b binding polypeptide of photosystem II (LHC II) were used to probe the effect of charged groups on the protein kinase activity of pea (Pisum sativum) thylakoid membranes. The effectiveness of the synthetic peptides as substrates for protein kinase activity or as inhibitors of LHC II phosphorylation was correlated with their net positive charge, which ranged between +2 and +5. The effects of the synthetic peptides on phosphorylation of other, non-LHC II, thyakoid polypeptides are also discussed.

An investigation of the substrate specificity of protein phosphatase 2C using synthetic peptide substrates; comparison with protein phosphatase 2A

The synthetic phosphopeptide RRATpVA was found to be the most effective substrate for protein phosphatase 2C (PP2C) so far identified. Replacement of phosphothreonine by phosphoserine decreased activity over 20-fold and a striking preference for phosphothreonine was also observed with two other substrates (RRSTpTpVA and casein) that were phosphorylated on both serine and threonine. Replacement of the C-terminal valine in RRATpVA by proline abolished dephosphorylation, while exchanging the N-terminal alanine by proline had no effect. The preference for phosphothreonine and the effect of proline are similar to protein phosphatase 2A (PP2A). However, the peptide RRREEETpEEEAA, an excellent substrate for PP2A, was not dephosphorylated by PP2C, and substitution of the C-terminal valine in RRATpVA by glutamic acid reduced the rate of dephosphorylation by PP2C over 10-fold, without affecting dephosphorylation by PP2A. Addition of two extra N-terminal arginine residues to RRASpVA increased PP2A catalysed dephosphorylation 4- to 5-fold, without altering dephosphorylation by PP2C. These results represent the first study of the specificity of PP2C using synthetic peptides, and strengthen the view that this approach may lead to the development of more effective and specific substrates for the serine/threonine-specific protein phosphatases.

Synthetic phosphopeptides are substrates for casein kinase II

Casein kinase II is a protein serine/threonine kinase that exhibits a preference for acidic substrates. Previous studies have demonstrated that a glutamic acid 3 amino acids C-terminal (+3) to a serine or threonine is required for phosphorylation. To examine the ability of phosphoserine and phosphothreonine residues to serve as specificity determinants for casein kinase II, phosphopeptides containing either of these phosphoamino acids in the +3 position were synthesized and tested as substrates. Phosphopeptides containing phosphoserine in the +3 position were readily phosphorylated. In contrast, corresponding phosphothreonine-containing peptides were very poorly phosphorylated. These results imply that prior phosphorylation of substrate proteins on serine, but not threonine residues, may II.

Structure of the Drosophila DNA topoisomerase II gene. Nucleotide sequence and homology among topoisomerases II

We have determined the nucleotide sequence of the Drosophila DNA topoisomerase II gene. Data from primer extension and S1 nuclease protection experiments were combined with comparisons of genomic and cDNA sequences to determine the structure of the mature messenger RNA. This message has a large open reading frame of 4341 nucleotides. The length of the predicted protein is 1447 amino acids with a molecular weight of 164,424. Topoisomerase II can be divided into three domains: (1) an N-terminal region with homology to the B (ATPase) subunit of the bacterial type II topoisomerase, DNA gyrase; (2) a central region with homology to the A (breaking and rejoining) subunit of DNA gyrase; (3) a C-terminal region characterized by alternating stretches of positively and negatively charged amino acids. DNA topoisomerase II from the fruit fly shares significant sequence homology with those from divergent sources, including bacteria, bacteriophage T4 and yeasts. The location and distribution of homologous stretches in these sequences are analyzed.

Phosphorylation of protein B-50 (GAP-43) from adult rat brain cortex by casein kinase II

The phosphoprotein B-50 (GAP-43) was purified from adult rat brain cortex and phosphorylated by casein kinase II. Phosphorylation of B-50 by casein kinase II approached 1.2 mol phosphate/mol B-50. The apparent Km of casein kinase II for B-50 was 4 microM with an apparent Vmax of 13 nmol.min-1.mg-1. A tryptic phosphopeptide map on reversed phase HPLC and phosphoamino acid analysis of [32P]B-50 showed that casein kinase II phosphorylated in serine residue(s) which were located in a single tryptic peptide. Phosphorylation of B-50 by casein kinase II was inhibited more than 90% by 5 micrograms heparin/ml or 2.4 mM peptide substrate specific for casein kinase II (RRREEETEEE). The initial phosphorylation rate was increased about 2-fold by 1 mM spermine.

Clathrin beta-light chain of rat liver coated vesicles is phosphorylated in vitro and in vivo

Clathrin beta-light chain of rat liver coated vesicles is phosphorylated in vitro in the presence of poly(L-lysine) by an endogenous protein kinase which appears to be similar to casein kinase II. Clathrin beta-light chain is also phosphorylated in vivo. After injection of [32P]phosphate into rats and preparation of purified coated vesicles in the presence of phosphatase inhibitors, electrophoretic analysis showed the presence of several labeled polypeptides including clathrin beta-light chain. A polypeptide of 50 kDa, which may correspond to the major polypeptide phosphorylated in vitro of coated vesicles, is also labeled in vivo.

Site specificity of casein kinase-2 (TS) from rat liver cytosol. A study with model peptide substrates

The factors determining the site recognition and phosphorylation by rat liver casein kinase-2 (CK-2) have been explored with a set of 14 related hexapeptides each including a single phosphorylatable amino acid and five acidic plus neutral residues. Such peptides are different from each other in the following features: the nature of the phosphorylatable amino acid, if any; its position relative to the critically required acidic residues; the extension and the structure of the acidic cluster. All of them were tested as substrate and/or competitive inhibitors of CK-2, and their kinetic and inhibition constants were determined. The results suggest the following conclusions. Under strictly comparable conditions Ser is by far preferred over Thr. Tyr not being affected at all. In order to carry out its role of structural determinant the critical acidic cluster must be located on the C-terminal side of the target residue, though not necessarily adjacent to it. The affinity for the protein-binding site, as deduced from Km and/or Ki values, is largely dependent on the number of acidic residues but it is also significantly enhanced if a hydroxylic residue is located on their N-terminal side. An acidic residue at position +3 relative to serine plays an especially important role for triggering phosphorylation, the peptide Ser-Glu-Glu-Ala-Glu-Glu having similar Km but negligible Vmax compared to Ser-Glu-Ala-Glu-Glu-Glu and Ser-Glu-Glu-Glu-Ala-Glu. These data provide a rationale for the substrate specificity of CK-2 and will give a helpful insight into the structure of the protein-binding site of this enzyme.

A type-1 casein kinase from yeast phosphorylates both serine and threonine residues of casein. Identification of the phosphorylation sites

A protein kinase (casein kinase 1A) active on casein and phosvitin but not on histones has been purified to near homogeneity from yeast cytosol and meets most criteria for being considered a type-1 casein kinase: it is a monomeric enzyme exhibiting an Mr of about 27 kDa by sucrose gradient centrifugation: it is not affected by inhibitors of type-2 casein kinases, such as heparin and polyglutamate, and shows negligible affinity for GTP. It also readily phosphorylates the residue Ser-22 of beta-casein located within the sequence -Ser(P)-Ser(P)-Ser(P)-Glu-Glu-Ser22-Ile-Thr-Arg- which is typically affected by casein kinases of the first class. On the other hand, casein kinase 1A displays the unusual property of phosphorylating threonine residue(s) in both whole casein and alpha s1-casein. The threonine residue phosphorylated in alpha s1-casein and accounting for most of the 32P incorporated into this protein by casein kinase 1A has been identified as Thr-49, which occurs in the sequence -Ser(P)-Glu-Ser(P)-Thr(P*)49-Glu-Asp-Gln-, whose two Ser(P) residues are already phosphorylated in the native protein. It is concluded that some type-1 casein kinases can also phosphorylate threonine residues provided they fulfil definite structural requirements, probably an acidic cluster near their N-terminal side.

Distinct structural requirements of Ca2+/phospholipid-dependent protein kinase (protein kinase C) and cAMP-dependent protein kinase as evidenced by synthetic peptide substrates

Protein kinase C, purified to near homogeneity from the brain, has been tested toward a variety of synthetic peptide substrates including different phosphorylatable residues. While it proved totally inactive toward the tyrosyl peptide Asp-Ala-Glu-Tyr-Ala-Ala-Arg-Arg-Arg-Gly, as well as toward several more or less acidic seryl peptides, it phosphorylates with a Ca2+/phospholipid-dependent mechanism, at seryl and/or threonyl residues, many basic peptides, some of which are also good substrates for cAMP-dependent protein kinase (A-kinase). Among the peptides tested, however, the best substrate for protein kinase C, with kinetic constants comparable to those of histones, is the nonapeptide Gly-Ser-Arg6-Tyr, which is not a substrate for A-kinase. Moreover, although the peptide Pro-Arg5-Ser-Ser-Arg-Pro-Val-Arg is a good substrate for both kinases, its derivative with ornitines replacing arginines is phosphorylated only by protein kinase C. Some typical substrates of A-kinase on the other hand, like the peptides Phe-Arg2-Leu-Ser-Ile-Ser-Thr-Glu-Ser and Arg2-Ala-Ser-Val-Ala, are phosphorylated by protein kinase C rather slowly and with unfavourable kinetic constants. It is concluded that, while both protein kinase C and A-kinase need basic groups close to the phosphorylatable residues, their primary structure determinants are quite distinct.

A synthetic peptide substrate specific for casein kinase II

A synthetic peptide having the sequence Arg-Arg-Arg-Glu-Glu-Thr-Glu-Glu-Glu was found to serve as a convenient substrate for the protein kinase generally referred to as casein kinase II. The enzyme exhibited an apparent Km of 500 microM for the peptide, as compared to an apparent Km of 50 microM for casein. The maximum velocities for phosphorylation of the peptide and of casein were similar. The peptide was not phosphorylated by any of eight other protein kinases, all of which were shown to be active toward their known substrates. The peptide was used to monitor activity during steps in the purification of casein kinase II from bovine liver. These experiments demonstrated that with this peptide it is now possible to obtain specific measurements of casein kinase II activity in crude enzyme preparations.