Insights Derived from the Structures of the Ser/Thr Phosphatases

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provided by Elsevier - Publisher Connector DL LOHSE, JM DENU AND JE DIXON MINIREVIEW Insights derived from the structures of the Ser/Thr phosphatases calcineurin and protein phosphatase 1 The crystal structures of serine/threonine phosphatases provide the basis for understanding their inhibition by physiologically relevant compounds such as microcystin, cyclosporin and FK506. The structures also highlight the importance of a common sequence motif found in a large family of metal-containing enzymes involved in phosphate ester hydrolysis.

Structure 15 October 1995, 3:987-990

There are numerous enzymes capable of hydrolyzing Structural features of the PPases phosphate esters [1]. The non-specific alkaline and acid The central feature of the structure of PPase-1 reported by phosphatases serve to recycle phosphate in metabolic Goldberg et al. [13] is the positioning of two metal ions by a reactions, and the protein phosphatases regulate signal- central 3-a-3---13 scaffold (Fig. la). These two metal ions transduction pathways. The protein phosphatases have appear to play both structural and catalytic roles in the phos- been divided into two large families on the basis of their phatases. The amino-acid residues highlighted in Figure lb substrate specificity. The family of protein-tyrosine are found at the intervening loops of this scaffold and phosphatases (PTPases) shows a preference for removing converge at the active site to participate in substrate recogni- phosphate from tyrosine and requires no metal ions for tion, to bind metal ions and to contribute to catalysis. This catalysis [2]. The PTPase family includes the dual- set of amino acids, and their spatial arrangement, is consis- specificity phosphatases which are capable of hydrolyzing tent with that seen in the calcineurin structure of Griffith et phosphorylated serine and threonine residues as well as al. [12]. Many of these residues are invariant in other mem- phosphorylated tyrosine. The Ser/Thr-specific protein bers of the PPase family, and are predicted to occupy similar phosphatases (PPases) are metal-requiring catalysts which loop regions [15]. The PPase-l structure described by share neither sequence identity nor structural similarities Egloff et al. (personal communication) was solved in the with the PTPases. presence of tungstate, an inhibitor that binds at the active site. Both Griffith's and Egloff's data support the concept PPase activity was first discovered in the conversion of the that, in contrast to the two-step reaction mechanism pro- active form of glycogen phosphorylase a to its inactive b posed for alkaline phosphatase and the PTPases [2], dephos- form (for a historical review see [3]). Since this discovery, phorylation by the PPases is catalyzed in a single step by a other PPases have been isolated, cloned, and characterized metal-activated water molecule. A plausible single-step [4-10]. These catalysts are regulated in a complex fashion mechanism, for example, would involve a water or hydrox- and have multiple biological functions [4-10]. The ide molecule (within 2.9 A of the phosphorous) acting as a amino-acid sequence of PPase-1, PPase-2A, and cal- bridge ligand between the two metals and positioned cineurin (PPase-2B), and an open reading frame in the directly in line with the P-O scissile bond of the substrate. bacteriophage (-PPase) all share limited identity with A histidine residue (His125 and Hisl51 in PPase-1 and cal- one another [11]. cineurin, respectively) would then be in the appropriate position to act as a general acid, donating a proton to the Recently, the three-dimensional structures of PPase-1 and oxygen atom on the leaving group of the phosphate ester calcineurin have been determined [12,13; M Egloff, D [12; Egloffet al., personal communication]. These structures Barford, P Deinemer and PTW Cohen, personal commu- are therefore consistent with an SN2 -type reaction which nication]. Core elements of the structures of Ser/Thr was suggested by mechanistic studies performed on phosphatases share similarity with corresponding elements calcineurin and purple-acid phosphatase [16,17]. of purple-acid phosphatase [14]. The structural features shared by these enzymes define residues important in The PPase-1 structure reported by Goldberg et al. [18] was metal binding and catalysis. The structure of PPase-1 was determined as a complex with the toxin microcystin, a solved as a complex with microcystin, a potent tumor pro- cyclic heptapeptide that obstructs the active site by binding moter [13]. Recent studies have demonstrated that to a hydrophobic groove that falls between the catalytic and calcineurin is the target of the immunosuppressive drugs regulatory domains. The sequences within this groove, cyclosporin A and FK506 [6]. The structure of calcineurin which are C-terminal to the conserved catalytic core, are was determined as a complex containing both, FK506, highly divergent among the phosphatases and, on the basis and the FK506 binding protein (FKBP). This information of structural and biological data, may be involved in their provides the foundation for designing improved drugs to regulation. A cyclin-dependent-kinase phosphorylation site aid organ transplantation. (Thr311 in PPase-1) within this region is conserved in

Fig. 1. Structure of Ser/Thr PPase 1. (a) Ribbon diagram of PPase-1 showing the -- 3-- metal-binding motif (in green), and bound metal ions (in blue). The inset shows a magnified view of the -a-x-a-3 metal-binding motif in the PPase-1 structure, highlighting the invariant amino acids involved in metal binding and/or catalysis. Numbers above the residues represent the decrease in reaction rate (kc ) when the individual amino acids were mutated in X-PPase [24]. (b) Invariant amino-acid residues involved in metal binding ancor catalysis of PPase-1, calcineurin A and X-PPase. The numbers in brackets represent the number of'unspecified amino acids. (Fig- ure provided by Drs. Kuriyan and Goldberg, Rockefeller University.)

Fig. 2. Ribbon structure of calcineurin ternary complex. Ribbon diagram showing the overall structure of the ternary complex of calcineurin A (blue), calcineurin B (green), FK506 (white) and the FK506-binding protein (red). The phosphate bound at the active site of calcineurin A is shown in yellow and the N-terminal myristate of calcineurin B is shown in purple. (Figure provided by James Griffith, and colleagues, Ver- tex Pharmaceuticals, Inc.) (Figure pro- duced from 112], with permission.]

several species and phosphorylation at this site inhibits extends away from the catalytic domain, is a five-turn activity in a cell-cycle-dependent manner [19,20]. amphipathic ot helix to which both calcineurin B and the FKBP-FK506 complex bind. The hydrophobic 'top half' Studies on the inhibition of calcineurin by cyclosporin A of the helix binds to a hydrophobic groove of calcineurin and FK506 have revealed the role for this enzyme in T-cell B, and the polar 'bottom half' forms a surface for inter- signaling [21]. The calcineurin structure (Fig. 2) [12] is a action with the FKBP-FK506 complex; the cyclosporin complex consisting of calcineurin A (catalytic subunit), A-cyclophilin complex also binds to the bottom half calcineurin B (regulatory subunit), FK506, and FKBP. The region [22]. The FKBP-FK506 complex does not contact calcineurin A structure has a 22-amino-acid extension that the active site, but inhibits dephosphorylation by physically is C-terminal to the active site and that comprises the cal- hindering substrate access and binding. This is consistent cineurin B binding helix (BBH). The BBH, which with studies which demonstrate that complex formation Ser/Thr phosphatases Lohse, Denu and Dixon 989

Fig. 3. The phosphoesterase motif. (a) Schematic diagram of the domain structures of the three PPases. The numbers refer to the (conserved) amino-acid residues that are used in metal binding and/or catalysis of PPase-1 [13], calcineurin (PPase 2B) 112] and the bacteriophage X protein phosphatase (X-PPase) 124]. The black boxes represent the catalytic domains of each enzyme, the white inserts are regions not involved in catalysis and the five colored boxes are the conserved amino-acid sequences which serve as a metallo-phosphoesterase motif. (b) Sequence alignment identifying the five distinct sequence motifs in the metallo-phosphoesterases. Each region is denoted by a different color. The aligned sequences and their accession numbers are: PPase-1, a PPase from rabbit skeletal muscle, P08129; calcineurin, a human PPase, P16298; X-PPase, a PPase from bacteriophage X, P03772; sit4 (PPase 1-1), a PPase from Saccharomyces cerevisiae, P20604; ret. deg. prot. (the retinal degeneration protein), a PPase from Drosophila melanogaster, P40421; PPase 2a-1, a PPase from Saccharomyces cerevisiae, P23594; purple-acid Pase, a purple acid phosphatase from kidney bean, P80366; human acid Pase, an atypical acid phosphatase from humans, PN0621; alkaline Pase, an alkaline phosphatase from Synechococcus sp., A47026; exo. sbcD E. co/i, an exonuclease from E.coli, P13457; exo. sbcD B. sub., an exonuclease from Bacillus subtilis, C39432; exo. T4, an exonuclease from bacteriophage T4, P04521; 5'-nuc. human, 5'-nucleoti- dase from human, P21589; diaden. tetra- Pase, diadenosine tetraphosphatase from E. coli, P05637; 2',3'-PDE, a 2',3'-cyclic- nucleotide 2'-phosphodiesterase from E. coli, A26398; UDP-sugar pyroPase, a UDP-sugar pyrophosphatase from E. coli, P07024; sphingo. PDE, a human sphin- gomyelin phosphodiesterase, S06957; RNA DBE, RNA intron lariat debranching enzyme from S. cerevisiae, P24309. X represents any amino acid, with the sub- scripts indicating the number of unspecified amino acids. (c) The active site of calcineurin showing the metallo-phosphoesterase binding motif. Conserved amino-acid residues are numbered and their coordination of Fe3+ (in blue) and Zn2+ (in yellow) is shown. Coordination is represented by the dotted lines. Atoms are color coded by element type: carbon in white, nitrogen in blue, oxygen in red, and phosphorous in purple. (Figure provided by James Griffith and colleagues, Vertex Pharmaceuticals, Inc.) (Part (c) reproduced from 112], with permission.) inhibits dephosphorylation of phosphopeptide substrates A metallo-phosphoesterase motif but allows a smaller artificial substrate, p-nitrophenyl- Alignment of the primary sequences of PPase-1, cal- phosphate, which is not excluded from the active site, to cineurin and the -PPase indicates that there are five be dephosphorylated. A similar strategy is employed by regions of conserved amino-acid sequence (Figure 3a). microcystin in its inhibition of PPase-1. It is interesting to These sequences are also found in other PPases, including note that the X-PPase that lacks any regulatory sequence is two yeast enzymes (sit 4 and PPase 2a-1) and a phos- not inhibited by the PPase inhibitors [23]. phatase involved in retinal degeneration in Drosophila 990 Structure 1995, Vol 3 No 10

melanogaster. The five conserved amino-acid sequences are Acknowledgements: This work was supported by grants from the not restricted to the Ser/Thr phosphatases (Fig. 3b). This National Institutes of Health and the Walther Cancer Institute. We motif is also found in kidney bean purple acid phosphatase would like to acknowledge Robert Baum for his assistance with the (KBPAP), an atypical acid and alkaline phosphatase, as well alignment of the phosphoesterases, John Kuriyan and David Bar- as bacterial exonucleases, a diadenosine tetraphosphatase, ford for sending us their manuscripts before publication and mem- bers of the Dixon laboratory for their comments and suggestions. phosphatases involved in sugar and lipid metabolism, and an enzyme involved in RNA debranching (Fig. 3b). The structures of calcineurin and PPase-1 suggest that, References 1. Boyer, P.D. & Krebs, E.G. (1986). The Enzymes (Vol. XVII), Academic together, these five conserved motifs play a role in catalysis Press, New York. and metal-ion binding in every member of the phospho- 2. Stone, R.L. & Dixon, J.E. (1994). Protein-tyrosine phosphatases. J. Biol. esterase family (PTPases and PPases). Chem. 269, 31323-31326. 3. Fischer, E.H. & Brautigan, D.L. (1982). A phosphatase by any other name: from prosthetic group removing enzyme to phosphorylase phos- Figure 3c shows the roles of these conserved residues in phatase. Trends Biochem. Sci. 7, 3-4. calcineurin. The active site contains a Zn2+/Fe3 + metal-ion 4. Cohen, P. (1989). The structure and function of protein phosphatases. Annu. Rev. of Biochem. 58, 453-508. pair and one phosphate ion. The zinc is coordinated by 5. Hunter, T. (1995). Protein kinases and phosphatases: the yin and yang Aspll8, Asnl50, His199, His281, and an oxygen of the of protein phosphorylation and signaling. Cell 80, 225-236. phosphate. 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This underscores the importance of the X-ray structures of Ser/Thr protein Daniel L Lohse, John M Denu and Jack E Dixon, Depart- phosphatases in our collective understanding of this family ment of Biological Chemistry, The University of Michigan of hydrolytic enzymes. Medical School, Ann Arbor, Michigan 48109-0606, USA.