Crystal structure of the complex formed between a group I Phospholipase A2 and a naturally occurring fatty acid at 2.7 Å resolution

Protein Science

Volumn 14, Issue 2, 2005, Pages 395-400

  Singh, Garima ^a   Jasti, Jayasankar ^a   Saravanan, K ^a   Sharma, Sujata ^a   Kaur, Punit ^a   Srinivasan, A ^a   Singh, Tej P ^a  

^a ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

Crystal structure; n tridecanoic acid; PLA2 complex; Regulation

Indexed keywords

AMINO ACID; ASPARTIC ACID; CALCIUM; COMPLEMENTARY DNA; DECANOIC ACID DERIVATIVE; FATTY ACID; PHOSPHOLIPASE A2; PROTEIN; SNAKE VENOM; SODIUM ION; WATER;

AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; CRYSTAL STRUCTURE; DNA SEQUENCE; ELECTRON; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REGULATORY MECHANISM; SNAKE;

ALKANES; AMINO ACID SEQUENCE; ANIMALS; ASPARTIC ACID; BUNGARUS; CALCIUM; CRYSTALLOGRAPHY, X-RAY; DICARBOXYLIC ACIDS; DNA, COMPLEMENTARY; ELECTRONS; FATTY ACIDS; HISTIDINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHOSPHOLIPASES A; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; SNAKE VENOMS; SODIUM; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

BUNGARUS CAERULEUS; SERPENTES;

EID: 13244292170     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.041115505     Document Type: Article

References (39)

1. Brünger, A.T. 1992. The free R-value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355: 472-474.
2. Brünger, A.T., Krukowski, A., and Erickson, J. 1990. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr. A 46: 585-593.
3. Brünger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, N., Pannu, N.S., et al. 1998. Crystallography and NMR system (CNS) A new software system for macromolecular structure determination. Acta Crystallogr. D 54: 905-921.
4. Cha, S.S., Lee, D., Adams, J., Kurdyla, J.T., Jones, C.S., Marshall, L.A., Bolognese, B., Abdel-Meguid, S.S., and Oh, B.H. 1996. High-resolution X-ray crystallography reveals precise binding interactions between human nonpancreatic secreted phospholipase A2 and a highly potent inhibitor (FPL67047XX). J. Med. Chem. 39: 3878-3881.
5. Chandra, V., Jasti, J., Kaur, P., Srinivasan, A., Betzel, Ch., and Singh, T.P. 2002a. Structural basis of phospholipase A2 inhibition for the synthesis of prostaglandins by the plant alkaloid aristolochic acid from a 1.7 Å crystal structure. Biochemistry 41: 10914-10919.
6. Chandra, V., Jasti, J., Kaur, P., Betzel, Ch., Srinivasan, A., and Singh, T.P. 2002b. First structural evidence of a specific inhibition of phospholipase A2 by α-tocopherol (vitamin E) and its implications in inflammation: Crystal structure of the complex formed between phospholipase A2 and α-tocopherol at 1.8 Å resolution. J. Mol. Biol. 320: 215-222.
7. Chandra, V., Jasti, J., Kaur, P., Dey, S., Perbandt, M., Srinivasan, A., Betzel, Ch., and Singh, T.P. 2002c. Crystal structure of a complex formed between a snake venom phospholipase A2 and a potent peptide inhibitor Phe-Leu-Ser-Tyr-Lys at 1.8 Å resolution. J. Biol. Chem. 277: 41079-41085.
8. Chandra, V., Jasti, J., Kaur, P., Dey, S., Srinivasan, A., Betzel, Ch., and Singh, T.P. 2002d. Design of specific peptide inhibitors of phospholipase A2: Structure of a complex formed between Russell's viper phospholipase A2 and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS). Acta Crystallogr. D 58: 1813-1819.
9. Collaborative Computational Project 4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D 50: 760-763.
10. Davidson, F.F. and Dennis, E.A. 1990. Evolutionary relationships and implications for the regulation of phospholipase A2: From snake venom to human secreted forms. J. Mol. Evol. 31: 228-238.
11. de Azevedo Jr., W.F., Ward, R.J., Gutierrez, J.M., and Arni, R.K. 1999. Structure of a Lys49-phospholipase A2 homologue isolated from the venom of Bothrops nummifer (jumping viper). Toxicon 37: 371-384.
12. Dennis, E.A. 1987. The Regulation of eicosanoid production: Role of phospholipases and inhibitors. BioTechnoloy 5: 1294-1300. (Reprinted in 1989. Biochimica Clinica 13: 215-223).
13. Dennis, E.A. 1987. The Regulation of eicosanoid production: Role of phospholipases and inhibitors. BioTechnoloy 5: 1294-1300. (Reprinted in 1989. Biochimica Clinica 13: 215-223).
14. Dodson, E.J., Winn, M., and Ralph, A. 1997. Collaborative Computational Project 4: Providing programs for protein crystallography. Methods Enzymol. 277: 620-633.
15. Engh, R.A. and Huber, R. 1991. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A 47: 392-400.
16. Esnouf, R.M. 1997. An extensively modified version of Molscript that includes greatly enhanced coloring capabilities. J. Mol. Graphics 15: 132-134.
17. Georgieva, D.N., Rypniewski, W., Gabdoulkhakov, A., Genov, N., and Betzel, C. 2004. Asp49 phospholipase A(2)-elaidoylamide complex: A new mode of inhibition. Biochem. Biophys. Res. Commun. 319: 1314-1321.
18. Hansford, K.A., Reid, R.C., Clark, C.I., Tyndall, J.D., Whitehouse, M.W., Guthrie, T., McGeary, R.P., Schafer, K., Martin, J.L., and Fairlie, D.P. 2003. D-Tyrosine as a chiral precusor to potent inhibitors of human non-pancreatic secretory phospholipase A2 (IIa) with anti-inflammatory activity. Chembiochem. 4: 181-185.
19. Heinrikson, R.L., Kruenger, E.T., and Keim, P.S. 1977. Amino acid sequence of phospholipase A2-α from the venom of Crotalus adamanteus. A new classification of phospholipases A2 based upon structural determinants. J. Biol. Chem. 252: 4913-4921.
20. Holland, D.R., Clancy, L.L., Muchmore, S.W., Ryde, T.J., Einspahr, H.M., Finzel, B.C., Heinrikson, RL., and Watenpaugh, K.D. 1990. The crystal structure of a lysine 49 phospholipase A2 from the venom of the cotton-mouth snake at 2.0 Å resolution. J. Biol. Chem. 265: 17649-17656.
21. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. 1991. Improved methods for building models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47: 110-119.
22. Kraulis, P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24: 946-950.
23. Laskowski, R., Macarthur, M., Moss, D., and Thornton, J. 1993. Procheck: A program to check stereochemical quality of protein structures. J. Appl. Crystallogr. 26: 283-290.
24. Lee, W.H., da Silva Giotto, M.T., Marangoni, S., Toyama, M.H., Polikarpov, I., and Garratt, R.C. 2001. Structural basis for low catalytic activity in Lys49 phospholipases A2-a hypothesis: The crystal structure of piratoxin II complexed to fatty acid. Biochemistry 40: 28-36.
25. Merritt, E.A. Raster 3D version 2.0: A program for photorealistic molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 50: 869-873.
26. Navaza, J. 1994. AmoRe: An automated package for molecular replacement. Acta Crystallogr. A 50: 157-163.
27. Otwinowski, Z. and Minor, W. 1997. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
28. Ramachandran, G.N. and Sasisekharan, V. 1968. Conformation of polypeptides and proteins. Adv. Protein Chem. 23: 283-438.
29. Schevitz, R.W., Bach, N.J., Carlson, D.G., Chirgadze, N.Y., Clawson, D.K., Dillard, R.D., Draheim, S.E., Hartley, L.W., Jones, N.D., and Mihelich, E.D. 1995. Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2. Nat. Struct. Biol. 2: 458-465.
30. Scott, D.L., Otwinowski, Z., Gelb, M.H., and Sigler, P.B. 1990. Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue. Science 250: 1563-1566.
31. Scott, D.L., White, S.P., Browning, J.L., Rosa, J.J., Gelb, M.H., and Sigler, P.B. 1991. Structures of free and inhibited human secretory phospholipase A2 from inflammatory exudates. Science 254: 1007-1010.
32. Sekar, K., Eswaramoorthy, S., Jain, M.K., and Sundaralingam, M. 1997. Crystal structure of the complex of bovine pancreatic phospholipase A2 with the inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycerol-2-phosphomethanol. Biochemistry 36: 14186-14191.
33. Sekar, K., Kumar, A., Liu, X., Tsai, M.D., Gelb, M.H., and Sundaralingam, M. 1998. Structure of the complex of bovine pancreatic phospholipase A2 with a transition-state analogue. Acta Cryst. D 54: 334-341.
34. Singh, G., Gourinath, S., Sharma, S., Paramasivam, M., Srinivasan, A., and Singh, T.P. 2001. Sequence and crystal structure determination of a basic phospholipase A2 from common krait (bungarus caeruleus) at 2.4 Å resolution: Identification and characterization of its pharmacological sites. J. Mol. Biol. 307: 1049-1059.
35. 2 from Naja naja sagittifera (group I) and a designed peptide inhibitor Val-Ala-Phe-Arg-Ser (VAFRS) at 1.9 Å resolution reveals unique features. Biochemistry 40: 11701-11706.
36. Thunnissen, M.M., Ab, E., Kalk, K.H., Drenth, J., Dijkstra, B.W., Kuipers, O.P., Dijkman, R., de Haas, G.H., and Verheij, H.M. 1990. X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor. Nature 347: 689-691.
37. van Deenen, L.L.M. and de Haas, G.H. 1963. The substrate specificity of phospholipase A2. Biochem. Biophys. Acta. 70: 538-553.
38. Verheij, H.M., Volwerk, J.J., Jansen, E.H., Puijk, W.C., Dijkstra, B.W., Drenth, J., and de Haas, G.H. 1980. Methylation of histidine-48 in pancreatic phospholipase A2. Role of histidine and calcium ion in the catalytic mechanism. Biochemistry 19: 743-750.
39. White, S.P., Scott, D.L., Otwinowski, Z., Gelb, M.H., and Sigler, P.B. 1990. Crystal structure of cobra-venom phospholipase A2 in a complex with a transition-state analogue. Science 250: 1560-1563.