Insights into the Catalytic Mechanism of PPM Ser/Thr Phosphatases from the Atomic Resolution Structures of a Mycobacterial Enzyme

Structure

Volumn 15, Issue 7, 2007, Pages 863-872

  Bellinzoni, Marco ^a   Wehenkel, Annemarie ^a   Shepard, William ^b   Alzari, Pedro M ^a  

^a INSTITUT PASTEUR   (France)

^b SYNCHROTRON SOLEIL   (France)

Author keywords

PROTEINS

Indexed keywords

ENZYME; LIGAND; METAL ION; PHOSPHATASE; SERINE THREONINE PHOSPHATASE PPM; SERINE THREONINE PHOSPHATASE PPP; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; DEPHOSPHORYLATION; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME SUBSTRATE COMPLEX; MOLECULAR MODEL; MYCOBACTERIUM SMEGMATIS; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION;

BACTERIAL PROTEINS; BINDING SITES; CATALYSIS; LIGANDS; MODELS, MOLECULAR; MYCOBACTERIUM SMEGMATIS; PHOSPHOPROTEIN PHOSPHATASE; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SERINE; THREONINE;

MYCOBACTERIUM SMEGMATIS;

EID: 34447299430     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.06.002     Document Type: Article

References (35)

1. Barford D. Molecular mechanisms of the protein serine/threonine phosphatases. Trends Biochem. Sci. 21 (1996) 407-412
2. Barford D., Das A.K., and Egloff M.P. The structure and mechanism of protein phosphatases: insights into catalysis and regulation. Annu. Rev. Biophys. Biomol. Struct. 27 (1998) 133-164
3. Benini S., Rypniewski W.R., Wilson K.S., Ciurli S., and Mangani S. Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism. J. Biol. Inorg. Chem. 6 (2001) 778-790
4. Boitel B., Ortiz-Lombardia M., Duran R., Pompeo F., Cole S.T., Cerveñansky C., and Alzari P.M. PknB kinase activity is regulated by phosphorylation in two Thr residues and dephosphorylation by PstP, the cognate phospho-Ser/Thr phosphatase, in Mycobacterium tuberculosis. Mol. Microbiol. 49 (2003) 1493-1508
5. Bork P., Brown N.P., Hegyi H., and Schultz J. The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues. Protein Sci. 5 (1996) 1421-1425
6. CCP4 (Collaborative Computational Project, Number 4). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50 (1994) 760-763
7. Chen G., Edwards T., D'Souza V.M., and Holz R.C. Mechanistic studies on the aminopeptidase from Aeromonas proteolytica: a two-metal ion mechanism for peptide hydrolysis. Biochemistry 36 (1997) 4278-4286
8. Cleland W.W., and Hengge A.C. Enzymatic mechanisms of phosphate and sulfate transfer. Chem. Rev. 106 (2006) 3252-3278
9. Cohen P. The structure and regulation of protein phosphatases. Annu. Rev. Biochem. 58 (1989) 453-508
10. Das A.K., Helps N.R., Cohen P.T., and Barford D. Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution. EMBO J. 15 (1996) 6798-6809
11. Egloff M.P., Cohen P.T., Reinemer P., and Barford D. Crystal structure of the catalytic subunit of human protein phosphatase 1 and its complex with tungstate. J. Mol. Biol. 254 (1995) 942-959
12. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 2126-2132
13. Fjeld C.C., and Denu J.M. Kinetic analysis of human serine threonine protein phosphatase 2C alpha. J. Biol. Chem. 274 (1999) 20336-20343
14. Gallego M., and Virshup D.M. Protein serine/threonine phosphatases: life, death, and sleeping. Curr. Opin. Cell Biol. 17 (2005) 197-202
15. Hengge A.C. Isotope effects in the study of enzymatic phosphoryl transfer reactions. FEBS Lett. 501 (2001) 99-102
16. Jackson M.D., and Denu J.M. Molecular reactions of protein phosphatases-insights from structure and chemistry. Chem. Rev. 101 (2001) 2313-2340
17. Jackson M.D., Fjeld C.C., and Denu J.M. Probing the function of conserved residues in the serine/threonine phosphatase PP2C alpha. Biochemistry 42 (2003) 8513-8521
18. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
19. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26 (1993) 795-800
20. Kennelly P.J. Protein kinases and protein phosphatases in prokaryotes: a genomic perspective. FEMS Microbiol. Lett. 206 (2002) 1-8
21. Kennelly P.J. Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry. Biochem. J. 370 (2003) 373-389
22. Lucast L.J., Batey R.T., and Doudna J.A. Large-scale purification of a stable form of recombinant tobacco etch virus protease. Biotechniques 30 (2001) 544-550
23. Mertz P., Yu L., Sikkink R., and Rusnak F. Kinetic and spectroscopic analyses of mutants of a conserved histidine in the metallophosphatases calcineurin and lambda protein phosphatase. J. Biol. Chem. 272 (1997) 21296-21302
24. Murshudov G.N., Vagin A.A., Lebedev A., Wilson K.S., and Dodson E.J. Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 247-255
25. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50 (1994) 157-163
26. Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., and Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127 (2006) 635-648
27. Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6 (1999) 458-463
28. Pohjanjoki P., Lahti R., Goldman A., and Cooperman B.S. Evolutionary conservation of enzymatic catalysis: quantitative comparison of the effects of mutation of aligned residues in Saccharomyces cerevisiae and Escherichia coli inorganic pyrophosphatases on enzymatic activity. Biochemistry 37 (1998) 1754-1761
29. Pullen K.E., Ng H.L., Sung P.Y., Good M.C., Smith S.M., and Alber T. An alternate conformation and a third metal in PstP/Ppp, the M. tuberculosis PP2C-family Ser/Thr protein phosphatase. Structure 12 (2004) 1947-1954
30. Rusnak F., and Mertz P. Calcineurin: form and function. Physiol. Rev. 80 (2000) 1483-1521
31. Schenk G., Gahan L.R., Carrington L.E., Mitic N., Valizadeh M., Hamilton S.E., de Jersey J., and Guddat L.W. Phosphate forms an unusual tripodal complex with the Fe-Mn center of sweet potato purple acid phosphatase. Proc. Natl. Acad. Sci. USA 102 (2005) 273-278
32. Sheldrick G.M., and Schneider T.R. SHELXL: high resolution refinement. Methods Enzymol. 277 (1997) 319-343
33. Swingle M.R., Honkanen R.E., and Ciszak E.M. Structural basis for the catalytic activity of human serine/threonine protein phosphatase-5. J. Biol. Chem. 279 (2004) 33992-33999
34. Voegtli W.C., White D.J., Reiter N.J., Rusnak F., and Rosenzweig A.C. Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes. Biochemistry 39 (2000) 15365-15374
35. Williams N.H. Models for biological phosphoryl transfer. Biochim. Biophys. Acta 1697 (2004) 279-287