Browse > Article
http://dx.doi.org/10.14348/molcells.2020.0192

Structural and Biochemical Characterization of the Two Drosophila Low Molecular Weight-Protein Tyrosine Phosphatases DARP and Primo-1  

Lee, Hye Seon (Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology)
Mo, Yeajin (Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology)
Shin, Ho-Chul (Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology)
Kim, Seung Jun (Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology)
Ku, Bonsu (Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology)
Publication Information
Molecules and Cells / v.43, no.12, 2020 , pp. 1035-1045 More about this Journal
Abstract
The Drosophila genome contains four low molecular weight-protein tyrosine phosphatase (LMW-PTP) members: Primo-1, Primo-2, CG14297, and CG31469. The lack of intensive biochemical analysis has limited our understanding of these proteins. Primo-1 and CG31469 were previously classified as pseudophosphatases, but CG31469 was also suggested to be a putative protein arginine phosphatase. Herein, we present the crystal structures of CG31469 and Primo-1, which are the first Drosophila LMW-PTP structures. Structural analysis showed that the two proteins adopt the typical LMW-PTP fold and have a canonically arranged P-loop. Intriguingly, while Primo-1 is presumed to be a canonical LMW-PTP, CG31469 is unique as it contains a threonine residue at the fifth position of the P-loop motif instead of highly conserved isoleucine and a characteristically narrow active site pocket, which should facilitate the accommodation of phosphoarginine. Subsequent biochemical analysis revealed that Primo-1 and CG31469 are enzymatically active on phosphotyrosine and phosphoarginine, respectively, refuting their classification as pseudophosphatases. Collectively, we provide structural and biochemical data on two Drosophila proteins: Primo-1, the canonical LMW-PTP protein, and CG31469, the first investigated eukaryotic protein arginine phosphatase. We named CG31469 as DARP, which stands for Drosophila ARginine Phosphatase.
Keywords
crystal structure; DARP; low molecular weight-protein tyrosine phosphatase; Primo-1; protein arginine phosphatase;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221.   DOI
2 Andersen, J.N., Mortensen, O.H., Peters, G.H., Drake, P.G., Iversen, L.F., Olsen, O.H., Jansen, P.G., Andersen, H.S., Tonks, N.K., and Moller, N.P. (2001). Structural and evolutionary relationships among protein tyrosine phosphatase domains. Mol. Cell. Biol. 21, 7117-7136.   DOI
3 Ardito, F., Giuliani, M., Perrone, D., Troiano, G., and Lo Muzio, L. (2017). The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review). Int. J. Mol. Med. 40, 271-280.   DOI
4 Caselli, A., Paoli, P., Santi, A., Mugnaioni, C., Toti, A., Camici, G., and Cirri, P. (2016). Low molecular weight protein tyrosine phosphatase: Multifaceted functions of an evolutionarily conserved enzyme. Biochim. Biophys. Acta 1864, 1339-1355.   DOI
5 Kolmodin, K. and Aqvist, J. (2001). The catalytic mechanism of protein tyrosine phosphatases revisited. FEBS Lett. 498, 208-213.   DOI
6 Ku, B., Keum, C.W., Lee, H.S., Yun, H.Y., Shin, H.C., Kim, B.Y., and Kim, S.J. (2016). Crystal structure of SP-PTP, a low molecular weight protein tyrosine phosphatase from Streptococcus pyogenes. Biochem. Biophys. Res. Commun. 478, 1217-1222.   DOI
7 Matthews, H.R. (1995). Protein kinases and phosphatases that act on histidine, lysine, or arginine residues in eukaryotic proteins: a possible regulator of the mitogen-activated protein kinase cascade. Pharmacol. Ther. 67, 323-350.   DOI
8 McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., and Read, R.J. (2007). Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674.   DOI
9 Miller, D.T., Read, R., Rusconi, J., and Cagan, R.L. (2000). The Drosophila primo locus encodes two low-molecular-weight tyrosine phosphatases. Gene 243, 1-9.   DOI
10 Otwinowski, Z. and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.   DOI
11 Schmidt, A., Trentini, D.B., Spiess, S., Fuhrmann, J., Ammerer, G., Mechtler, K., and Clausen, T. (2014). Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response. Mol. Cell. Proteomics 13, 537-550.   DOI
12 Hatzihristidis, T., Desai, N., Hutchins, A.P., Meng, T.C., Tremblay, M.L., and Miranda-Saavedra, D. (2015). A Drosophila-centric view of protein tyrosine phosphatases. FEBS Lett. 589, 951-966.   DOI
13 Elsholz, A.K., Turgay, K., Michalik, S., Hessling, B., Gronau, K., Oertel, D., Mader, U., Bernhardt, J., Becher, D., Hecker, M., et al. (2012). Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc. Natl. Acad. Sci. U. S. A. 109, 7451-7456.   DOI
14 Emsley, P. and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132.   DOI
15 Fjeld, C.C., Rice, A.E., Kim, Y., Gee, K.R., and Denu, J.M. (2000). Mechanistic basis for catalytic activation of mitogen-activated protein kinase phosphatase 3 by extracellular signal-regulated kinase. J. Biol. Chem. 275, 6749-6757.   DOI
16 Tonks, N.K. (2006). Protein tyrosine phosphatases: from genes, to function, to disease. Nat. Rev. Mol. Cell Biol. 7, 833-846.   DOI
17 Fonseca, E.M., Trivella, D.B., Scorsato, V., Dias, M.P., Bazzo, N.L., Mandapati, K.R., de Oliveira, F.L., Ferreira-Halder, C.V., Pilli, R.A., Miranda, P.C., et al. (2015). Crystal structures of the apo form and a complex of human LMWPTP with a phosphonic acid provide new evidence of a secondary site potentially related to the anchorage of natural substrates. Bioorg. Med. Chem. 23, 4462-4471.   DOI
18 Fuhrmann, J., Mierzwa, B., Trentini, D.B., Spiess, S., Lehner, A., Charpentier, E., and Clausen, T. (2013). Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria. Cell Rep. 3, 1832-1839.   DOI
19 Fuhrmann, J., Subramanian, V., Kojetin, D.J., and Thompson, P.R. (2016). Activity-based profiling reveals a regulatory link between oxidative stress and protein arginine phosphorylation. Cell Chem. Biol. 23, 967-977.   DOI
20 Hay, I.M., Fearnley, G.W., Rios, P., Kohn, M., Sharpe, H.J., and Deane, J.E. (2020). The receptor PTPRU is a redox sensitive pseudophosphatase. Nat. Commun. 11, 3219.   DOI
21 Zhang, Z.Y., Wang, Y., and Dixon, J.E. (1994). Dissecting the catalytic mechanism of protein-tyrosine phosphatases. Proc. Natl. Acad. Sci. U. S. A. 91, 1624-1627.   DOI
22 Hong, S.B., Lubben, T.H., Dolliver, C.M., Petrolonis, A.J., Roy, R.A., Li, Z., Parsons, T.F., Li, P., Xu, H., Reilly, R.M., et al. (2005). Expression, purification, and enzymatic characterization of the dual specificity mitogen-activated protein kinase phosphatase, MKP-4. Bioorg. Chem. 33, 34-44.   DOI
23 Hunter, T. (1995). Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell 80, 225-236.   DOI
24 Trentini, D.B., Suskiewicz, M.J., Heuck, A., Kurzbauer, R., Deszcz, L., Mechtler, K., and Clausen, T. (2016). Arginine phosphorylation marks proteins for degradation by a Clp protease. Nature 539, 48-53.   DOI
25 Wakim, B.T. and Aswad, G.D. (1994). Ca2+-calmodulin-dependent phosphorylation of arginine in histone 3 by a nuclear kinase from mouse leukemia cells. J. Biol. Chem. 269, 2722-2727.   DOI
26 Yun, H.Y., Lee, J., Kim, H., Ryu, H., Shin, H.C., Oh, B.H., Ku, B., and Kim, S.J. (2018). Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1. PLoS One 13, e0197635.   DOI
27 Zhou, B. and Zhang, Z.Y. (1999). Mechanism of mitogen-activated protein kinase phosphatase-3 activation by ERK2. J. Biol. Chem. 274, 35526-35534.   DOI