Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 Å resolution

Structure

Volumn 6, Issue 4, 1998, Pages 511-519

  Wei, Yunyi ^a,e   Swenson, Lora ^b   Castro, Clementina ^c   Derewenda, Urszula ^a   Minor, Wladek ^a   Arai, Hiroyuki ^d   Aoki, Junken ^d   Inoue, Keizo ^d   Servin Gonzalez, Luis ^c   Derewenda, Zygmunt S ^a  

^a UNIVERSITY OF VIRGINIA HEALTH SYSTEM   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

^c INSTITUTO DE INVESTIGACIONES BIOMÉDICAS   (Mexico)

^d UNIVERSITY OF TOKYO   (Japan)

^e VERTEX PHARMACEUTICALS   (United States)

Author keywords

Acetylhydrolase; Enzyme structure; Lipase; hydrolase

Indexed keywords

EID: 13144279300     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00052-5     Document Type: Article

References (54)

1. Venable, M.E., Zimmerman, G.A., McIntyre, T.M. & Prescott, S.M. (1993). Platelet-activating factor: a phospholipid autacoid with diverse actions. J. Lipid Res. 34, 691-702.
2. O'Flaherty, J.T. & Wykle, R.L. (1989). PAF and cell activation. In Platelet activating factor and human disease. (Barnes, P.J., Page, C.P. & Henson, P., eds.), pp. 117-137, Blackwell Scientific Publications, Oxford, UK.
3. El Azzouzi, B., Jurgens, P., Beneviste, P. & Thomas, Y. (1993). Immunoregulatory functions of PAF-acether. IX. Modulation of apoptosis in an immature T-cell line. Biochem. Biophys. Res. Commun 190, 320-324.
4. Shukla, D. (1992). Platelet-activating factor receptor and signal transduction mechanisms. FASEB J. 6, 2296-2301.
5. Bennett, S.A., Leite, L.C. & Birnboim, H.C. (1993). Platelet-activating factor, an endogenous mediator of inflammation, induces phenotypic transformation of rat embryo cells. Carcinogenesis 14, 1289-1296.
6. Bazan, N.G. & Rodriguez de Turco, E.B. (1995). Platelet-activating factor is a synapse messenger and a modulator of gene expression in the nervous system. Neurochem. Int. 26, 435-441.
7. Kumar, R., Harvey, S., Kester, N., Hanahan, D. & Olson, M. (1988). Production and effects of platelet-activating factor in the rat brain. Biochim. Biophys. Acta 963, 375-383.
8. Panetta, T., Marcheselli, V.L., Braquet, P., Spinnewyn, B. & Bazan, N.G. (1987). Effects of a platelet-activating factor antagonist (BN52021) on free fatty acids, diacylglycerols, polyphosphoinositides and blood flow in the gerbil brain: inhibition of ischemia reperfusion induced cerebral injury. Biochem. Biophys. Res. Commun 149, 580-587.
9. Kato, K., Clark, G.D., Bazan, N.G. & Zorumski, C.F. (1994). Platelet-activating factor as a potential retrograde messenger in CA1 hippocampal long-term potentiation. Nature 367, 175-179.
10. Stafforini, D.M., Prescott, S.M., Zimmerman, G.A. & McIntyre, T.M. (1996). Mammalian platelet-activating factor acetylhydrolases. Biochim. Biophys. Acta 1301, 161-173.
11. Stafforini, D.M., McIntyre, T.M., Zimmerman, G.A. & Prescott, S.M. (1997). Platelet-activating factor acetylhydrolases. J. Biol. Chem. 272, 17895-17898.
12. Hattori, M., Adachi, H., Tsujimoto, M., Arai, H. & Inoue, K. (1994). The catalytic subunit of bovine brain platelet-activating factor acetylhydrolase is a novel type of serine esterase. J. Biol. Chem. 269, 23150-23155.
13. Hattori, M., Adachi, H., Aoki, J., Tsujimoto, M., Arai, K. & Inoue, K. (1995). Cloning and expression of a cDNA encoding the β subunit (30kDa subunit) of bovine brain platelet-activating factor acetylhydrolase. J. Biol. Chem. 270, 31345-31352.
14. Hattori, M., Adachi, H., Tsujimoto, M., Arai, H. & Inoue, K. (1994). Miller-Dieker lissencephaly gene encodes a subunit of brain platelet-activating factor acetylhydrolase. Nature 370, 216-218.
15. Ho, Y.S., et al., & Derewenda, Z.S. (1997). Brain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer. Nature 384, 89-93.
16. Tjoelker, L.W., et al., & Gray, P.W. (1995). Anti-inflammatory properties of a platelet-activating factor acetylhydrolase. Nature 374, 549-552.
17. Hattori, K., et al., & Inoue, K. (1996). cDNA cloning and expression of intracellular platelet-activating factor (PAF) acetylhydrolase II. J. Biol. Chem. 271, 33032-33038.
18. Derewenda, Z.S. & Derewenda, U. (1991). Relationships among serine hydrolases: evidence for a common structural motif in triacylglycerol lipases and esterases. Biochem. Cell Biol. 69, 842-851.
19. Ollis, D.L., et al., & Goldman, A. (1992). The α/β hydrolase fold. Protein Eng. 5, 597-611.
20. Tjoelker, L.W., et al., & Gray, P.W. (1995). Plasma platelet-activating factor acetylhydrolase is a secreted phospholipase A2 with a catalytic triad. J. Biol. Chem. 270, 25481-25487.
21. Hattori, K., Hattori, M., Adachi, H., Tsujimoto, M., Arai, H. & Inoue, K. (1995). Purification and characterization of platelet-activating factor acetylhydrolase II from bovine liver cytosol. J. Biol. Chem. 270, 22308-22313.
22. Lawson, D.M., et al., & Derewenda, Z.S. (1994). Structure of a myristoyl-ACP-specific thioesterase from Vibrio harveyi. Biochemistry 33, 9382-9388.
23. Verschueren, K.H., Franken, S.M., Rozeboom, H.J., Kalk, K.H. & Dijkstra, B.W. (1993). Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism. J. Mol. Biol. 232, 856-872.
24. Hecht, H.J., Sobek, H., Haag, T., Pfeifer, O. & van Pee, K.H. (1994). The metal-ion-free oxidoreductase from Streptomyces aureofaciens has an α/β hydrolase fold. Nat. Struct. Biol. 1, 532-537.
25. Derewenda, Z.S. & Wei, Y. (1995). Molecular mechanism of enantiorecognition by esterases. J. Am. Chem. Soc. 117, 2104-2105.
26. Brzozowski, A.M., et al., & Thim, L. (1991). A model for interfacial activation in lipases from the structure of a fungal lipase - inhibitor complex. Nature 352, 491-494.
27. Derewenda, U., Brzozowski, A.M., Lawson, D.M. & Derewenda, Z.S. (1992). Catalysis at the interface: the anatomy of a conformational change in a triglyceride lipase. Biochemistry 31, 1532-1541.
28. van Tilbeurgh, H., Egloff, M.-P., Martinez, C., Rygani, N., Verger, R. & Cambillau, C. (1993). Interfacial activation of the lipase-prolipase complex by mixed micelles revealed by X-ray crystallography. Nature 362, 814-820.
29. Martinez, C., et al., & Cambillau, C. (1994). Cutinase, a lipolytic enzyme with a preformed oxyanion hole. Biochemistry 33, 83-89.
30. Longhi, S., Czjzek, M., Lamzin, V., Nicolas, A. & Cambillau, C. (1997). Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis. J. Mol. Biol. 268, 779-799.
31. Derewenda, U., et al., & Derewenda, Z.S. (1994). An unusual buried polar cluster in a family of fungal lipases. Nat. Struct. Biol. 1, 36-47.
32. Schrag, J.D., Winkler, F.K. & Cygler, M. (1992). Pancreatic lipases: evolutionary intermediates in a positional change of catalytic carboxylates? J. Biol. Chem. 267, 4300-4303.
33. Pathak, D. & Ollis, D. (1990). Refined structure of dienelactone hydrolase at 1.8 A. J. Mol. Biol. 214, 497-525.
34. Schrag, J.D., Li, Y., Wu, S. & Cygler, M. (1991). Ser-His-Glu triad forms the catalytic site of the lipase from Geotrichum candidum. Nature 351, 761-764.
35. Grochulski, P., et al., & Cygler, M. (1993). Insights into interfacial activation from an open structure of Candida rugosa lipase. J. Biol. Chem. 268, 12843-12847.
36. Winkler, F.K., d'Arcy, A. & Hunziker, W. (1990). Structure of human pancreatic lipase. Nature 343, 771-774.
37. Hide, W.A., Chan, L. & Li, W.H. (1992). Structure and evolution of the lipase superfamily. J. Lipid Res. 33, 167-178.
38. Hjorth, A., et al., & Verger, R. (1993). A structural domain (the lid) found in pancreatic lipases is absent in the guinea pig (phospho)lipase. Biochemistry 32, 4702-4707.
39. Withers-Martinez, C., Carriere, F., Verger, R., Bourgeois, D. & Cambillau, C. (1996). A pancreatic lipase with a phospholipase A1 activity: crystal structure of a chimeric pancreatic lipase-related protein 2 from guinea pig. Structure 4, 1363-1374.
40. King, T.P., Lu, G., Gonzalez, M., Qian, N. & Soldatova, L. (1996). Yellow jacket venom allergens, hyaluronidase and phospholipase: sequence similarity and antigenic cross-reactivity with their hornet and wasp homologs and possible implications for clinical allergy. J. All. Clin. Immunol. 98, 588-600.
41. Soldatova, L., Kochoumian, L. & King, T.P. (1993). Sequence similarity of a hornet (D. maculata) venom allergen phospholipase A1 with mammalian lipases. FEBS Lett. 320, 145-149.
42. Thirstrup, K., Verger, R. & Carriere, F. (1994). Evidence for a pancreatic lipase subfamily with new kinetic properties. Biochemistry 33, 2748-2756.
43. Stafforini, D.M., Prescott, S.M. & McIntyre, T.M. (1987). Human plasma platelet-activating factor acetylhydrolase. Purification and properties. J. Biol. Chem. 262, 4223-4230.
44. Stremler, K.E., Stafforini, D.M., Prescott, S.M. & McIntyre, T.M. (1991). Human plasma platelet-activating factor acetylhydrolase. Oxidatively fragmented phospholipids as substrates. J. Biol. Chem. 266, 11095-11103.
45. Stafforini, D.M., et al., & Prescott, S.M. (1996). Platelet-activating factor acetylhydrolase deficiency. A missense mutation near the active site of an anti-inflammatory phospholipase. J. Clin. Invest. 97, 2784-2791.
46. Yamada, Y. & Yokota, M. (1997). Loss of activity of plasma platelet-activating factor acetylhydrolase due to a novel Gln281→Arg mutation. Biochem. Biophys. Res. Commun. 236, 772-775.
47. Perez, C., Juarez, K., Garcia-Castells, E., Soberon, G. & Servin-Gonzalez, L. (1993). Cloning, characterization, and expression in Streptomyces lividans 66 of an extracellular lipase-encoding gene from Streptomyces sp. M11. Gene 123, 109-114.
48. Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzym. A 276, 307-326.
49. CCP4. (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50, 760-763.
50. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for binding protein models in electron density maps and the location of errors in these models. A47, 110-119.
51. Navaza, J. (1994). AMORE: an automated package for molecular replacement. Acta Cryst. A 50, 157-163.
52. Brunger, A. (1992). X-PLOR, version 3.1. A system for X-ray crystallography and NMR. Yale University Press, New Haven, CT.
53. Laskowski, R.A., McArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 282-291.
54. Carson, M. (1991). Ribbons 2.0. J. Appl. Cryst. 24, 958-961.