REVIEW ARTICLE Protein tyrosine phosphatase structure–function relationships in regulation and pathogenesis Frank Bo¨ hmer1, Stefan Szedlacsek2, Lydia Tabernero3, Arne O¨ stman4 and Jeroen den Hertog5,6 1 Center for Molecular Biomedicine, Jena University Hospital, Germany 2 Institute of Biochemistry of the Romanian Academy, Bucharest, Romania 3 Faculty of Life Sciences, University of Manchester, Manchester, UK 4 Cancer Center Karolinska, Karolinska Institutet, Stockholm, Sweden 5 Hubrecht Institute – KNAW and University Medical Center Utrecht, The Netherlands 6 Institute of Biology Leiden, Leiden University, The Netherlands Keywords Protein phosphorylation on tyrosine residues is tightly controlled by pro- oxidation; pathogenesis; protein tyrosine tein tyrosine phosphatases (PTPs) at multiple levels: spatio-temporal phosphatase; regulation; structure-function expression, subcellular localization and post-translational modification. Structural and functional analysis of the PTP domains has provided insight Correspondence Jeroen den Hertog, Hubrecht Institute, into catalysis and regulatory mechanisms that control the enzymatic activ- Uppsalalaan 8, 3584 CT Utrecht, ity. Understanding the molecular basis of PTP regulation is of fundamental The Netherlands importance to dissect the pleiotropic effect of these enzymes in both health Fax: +31 30 2516464 and disease. Here, we review recent insights into the regulation of receptor- Tel: +31 30 2121800 like PTPs by extracellular ligands and into regulation by reversible oxida- E-mail: [email protected] tion that impairs catalysis directly. The physiological roles of PTPs are essential in homeostasis in eukaryotic cells and pertubation of their func- (Received 27 February 2012, revised 18 May 2012, accepted 4 June 2012) tional attributes causes different disease states. As an example, we discuss recent findings indicating how inappropriate oxidation of PTPs in cancer doi:10.1111/j.1742-4658.2012.08655.x cells may contribute to cell transformation. On the other hand, PTPs from many pathogens are key virulence factors and manipulate signalling path- ways in the host cells to promote invasion and survival of the microorgan- isms. This research area has received relatively little attention but has advanced remarkably. We review the structural features of pathogenic PTPs, their similarities and differences with eukaryotic PTPs, and the possible exploitation of this knowledge for therapeutic intervention. Structures of PTPs Analysis of protein tyrosine phosphatase (PTP) struc- much attention as candidate drug targets. We focus on tures is not only important for understanding their Cys-based PTPs [1] and discuss novel insights in PTP function and regulation but also for identifying strate- structure which may be important for pharmacological gies for pharmacological modulation of PTP activity. modulation, and emphasize novel findings and contro- Given the progress in establishing PTP deregulation in versial issues for transmembrane (receptor-like) PTPs different pathologies such as cancer, PTPs deserve (RPTPs). Abbreviations AML, acute myeloid leukaemia; DUSP, dual specificity PTP; FLT3, Fms-like tyrosine kinase 3; FLT3 ⁄ ITD, internal tandem duplication of FLT3; LMWPTP, low molecular weight PTP; PDGF, platelet-defined growth factor; Prx, peroxiredoxin; PTP, protein tyrosine phosphatase; PTPLP, PTP-like phytase; ROS, reactive oxygen species; RPTP, transmembrane PTP; RTK, receptor tyrosine kinase; YopH, Yersinia outer protein H. FEBS Journal 280 (2013) 413–431 ª 2012 The Authors Journal compilation ª 2012 FEBS 413 Protein tyrosine phosphatase structure-function F. Bo¨ hmer et al. [5,12]. The WPD aspartic acid is positioned far out of PTP structures: similar at the core, yet many the active site, which may facilitate the design of variations beyond that potent inhibitors. Bidentate inhibitors binding two dif- PTP1B was the first PTP for which the crystal struc- ferent sites on the same PTP molecule have much ture was solved [2]. In addition, the crystal structure of higher specificities and lower binding constants. Effi- a PTP1B–substrate complex [3] provided structural cient bidentate modulators were obtained for Lyp, a insight into the molecular basis of PTP-mediated potential target for many autoimmune disorders [13], dephosphorylation for the first time. The crystal struc- SHP-1, with an important role in hematopoietic cell ture of the first dual specificity PTP (DUSP) demon- functions [14], and YopH, a virulence factor of Yer- strated why DUSPs can dephosphorylate pTyr as well sinia pestis, the causative agent of the plague [15,16]. as pSer and pThr, because the catalytic site is shal- Good insight into the structural features of PTPs facil- lower in the DUSPs than in pTyr-specific PTPs. The itates the design of specific PTP inhibitors. shorter side-chains of pSer and pThr can reach the cat- alytic site cysteine in DUSPs but not in PTPs [4]. The Dimerization of RPTPs crystal structure of the membrane-proximal PTP domain of RPTPa shows a similar fold to PTP1B, and RPTPa-D1 formed dimers in the crystal structure, in a by now it is evident that the active sites of all classical manner that suggested dimer-induced inactivation of PTPs have highly conserved core structures [5,6]. In RPTPa because a helix–loop–helix wedge-like structure fact, the core structure of PTPs from microorganisms to the N-terminal side of one of the protomers is similar to eukaryotic PTPs as well (see below). occluded the catalytic site and vice versa [17]. It is broadly accepted that protein tyrosine kinases are acti- vated by oligomerization in the presence or absence of Small molecule PTP inhibitors an activating ligand [18]. By analogy, it is an attractive The design of active-site-directed small molecules with idea that RPTPs are also regulated by oligomerization high specificity to a given PTP is severely hampered by [17,19]. There are numerous reports supporting or con- the similarity in structure. Nevertheless, high through- tradicting this hypothesis [20]. Barr et al. [5] have put in silico screens for inhibitors of Shp2, known to recently reported, based on structural and biophysical be a bona fide oncogene involved in several types of analysis, that single and tandem PTP domains do not leukaemia, identified phenylhydrazonopyrazolone sul- form dimers in physiological buffers. They also showed fonate as a potent and cell-permeable inhibitor display- that the reciprocal orientation of the catalytic D1 ing high specificity for Shp2 over the related tyrosine domain and the non-catalytic D2 domain is highly phosphatases Shp1 and PTP1B [7]. Highly potent and conserved and does not fit with the inhibitory wedge selective inhibitors were also found for PTP1B. One of model. On the other hand, there is a multitude of data the most efficient is a difluoromethylphosphonate supporting that many RPTPs, like RPTPa, GLEPP1, derivative, proved to be competitive and tight-binding RPTPr, Sap-1, CD45 and RPTPe dimerize in living (Ki = 2.4 nm) with over 10-fold selectivity over the cells and that dimerization regulates their activity [21– most closely related PTP, TCPTP, and more than 600- 27]. Moreover, dimer formation of GLEPP1 and fold selectivity over other PTPs [8]. Another recently RPTPe in living cells involves their intracellular reported inhibitor of PTP1B is trodusquemine, a natu- regions [23,27]. Dimer formation may involve both ral product isolated from dogfish shark which showed homotypic D1–D1, D2–D2 interactions and hetero- non-competitive inhibition kinetics on PTP1B and, typic D1–D2 interactions, in a specific manner for each remarkably, over 200-fold preference against TCPTP dimer. In the case of RPTPe dimer formation the [9,10]. D1–D1 interactions are weak while the D2–D2 interac- In the context of a highly conserved active site, iden- tions are strong and have a major contribution to tification of allosteric binding sites is of particular dimerization [27]. The contribution to dimerization is interest. Recently an allosteric site was identified in the not limited to D1 and D2. Other regions of PTPs con- vicinity of the catalytic WPD loop of RPTPc [11]. It is tribute to dimerization too. For instance, RPTPa di- a small hydrophobic pocket and several specific inhibi- merizes constitutively in living cells, which is mediated tors bound to this site, thus perturbing the WPD loop by multiple domains [22,28]. The apparent contradic- and inducing a novel ‘superopen’ conformation. Ear- tion with Barr et al. [5] may be explained if one lier reports mentioned an ‘atypical’ open state of the assumes that the flexible linker between the two intra- catalytic WPD loop in three PTPs, STEP, LYP and cellular domains allows reorientation of D1 and D2. GLEPP1, corresponding to an inactive conformation However, the crystal structures of the D1–D2 domains 414 FEBS Journal 280 (2013) 413–431 ª 2012 The Authors Journal compilation ª 2012 FEBS F. Bo¨ hmer et al. Protein tyrosine phosphatase structure-function of PTP-LAR and CD45 indicate extensive interdomain potential to signal across the membrane from the interactions, suggesting limited flexibility of the relative inside out [36]. orientation of D1–D2 in solution. Much progress has been made in the structural anal- As indicated above, not only the cytoplasmic ysis of the ectodomains of RPTPs. For instance, the domain but also the transmembrane region and ⁄ or the RPTPl ectodomains interact in a homophilic manner proximal, hydrophobic region frequently seem to play when expressed on opposing cells and this interaction a role in dimer formation, as in the case of PTPBR7, actually determines the distance between the two adja- PTP-SL [29], GLEPP1 [23] and Sap-1 [24]. There are a cent cells [37]. Moreover, the structures of the proteo- couple of poorly conserved elements in the transmem- glycan binding site in the ectodomain of RPTPr brane region which may have a function. Alignment of provided insight into the proteoglycan-induced molecu- the membrane-spanning sequences of 20 human lar switch for RPTPr clustering [38]. RPTPs shows that two hydrophobic amino acids, iso- The functional consequences of RPTP dimerization leucine and valine, are by far the most frequent resi- vary from RPTP to RPTP.