Crystal structure of coagulation factor IX-binding protein from habu snake venom at 2.6 Å: Implication of central loop swapping based on deletion in the linker region

Journal of Molecular Biology

Volumn 289, Issue 1, 1999, Pages 103-112

  Mizuno, Hiroshi ^a   Fujimoto, Zui ^a   Koizumi, Mika ^a   Kano, Hiromi ^a   Atoda, Hideko ^b   Morita, Takashi ^b  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b MEIJI PHARMACEUTICAL UNIVERSITY   (Japan)

Author keywords

C type lectin; Ca2+ binding; Coagulation factor IX binding protein; Crystal structure; Domain swapping

Indexed keywords

BINDING PROTEIN; BLOOD CLOTTING FACTOR 9; CALCIUM BINDING PROTEIN; CALCIUM ION; COAGULATION FACTOR IX BINDING PROTEIN; LECTIN; PROTEIN SUBUNIT; SNAKE VENOM; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; DIMERIZATION; DISULFIDE BOND; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STEREOCHEMISTRY; X RAY CRYSTALLOGRAPHY;

EID: 0033612377     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2756     Document Type: Article

References (43)

1. Aragon-Ortiz F., Mentele R., Auerswald E. A. Amino acid sequence of a lectin-like protein from Lachesis muta stenophyrs venom. Toxicon. 34:1996;763-769.
2. Atoda E., Morita T. A novel blood coagulation factor IX/factor X-binding protein with anticoagulant activity from the venom ofTrimeresurus flavoviridis (habu snake): isolation and characterization. J. Biochem. 106:1989;808-813.
3. Atoda H., Hyuga M., Morita T. The primary structure of coagulation factor IX/factor X-binding protein isolated from the venom of Trimeresurus flavoviridis: homology with asialoglycoprotein receptors, proteoglycan core protein, tetranectin, and lymphocyte Fcε receptor for immunoglobulin E. J. Biol. Chem. 266:1991;14903-14911.
4. Atoda H., Ishikawa M., Yoshihara E., Sekiya F., Morita T. Blood coagulation factor IX-binding protein from the venom of Trimeresurus flavoviridis purification and characterization. J. Biochem. 118:1995;965-973.
5. Atoda H., Ishikawa M., Mizuno H., Morita T. Coagulation factor X-binding protein from Deinagkistrodon acutus venom is a Gla-domain-binding protein. Biochemistry. 37:1998;17361-17370.
6. Bennett M. J., Schlunegger M. P., Eisenberg D. 3D domain swapping: a mechanism for oligomer assembly. Protein Sci. 4:1995;2455-2468.
7. Bertrand J. A., Pignol D., Bernard J.-P., Verdier J.-M., Dagorn J.-C., Fontecilla-Camps J. C. Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation. EMBO J. 15:1996;2678-2684.
8. Brünger A. T. X-PLOR (Version 3.1) A System for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven CT and London.
9. Chen Y.-L., Tsai I.-H. Functional and sequence characterization of coagulation factor IX/factor X-binding protein from the venom ofEchis carinatus leucogaster. Biochemistry. 35:1996;5264-5271.
10. 2+-dependent animal lectins. Prog. Nucl. Acid Res. Mol. Biol. 45:1993;207-232.
11. Fujimura Y., Titani K., Usami Y., Suzuki M., Oyama T., Matsui T., Fukui H., Sugimoto M., Ruggeri Z. M. Isolation and chemical characterization of two structurally and functionally distinct forms of botrocetin, the platelet coagglutinin isolated from the venom of Bothrops jararaca. Biochemistry. 30:1991;1957-1964.
12. Fujimura Y., Ikeda Y., Miura S., Yoshida E., Shima H., Nishida S., Suzuki M., Titani K., Taniuchi Y., Kawasaki T. Isolation and characterization of jararaca GPIb-BP, a snake venom antagonist specific to platelet glycoprotein Ib. Thromb. Haemostas. 74:1995;743-750.
13. Furey W., Swaminathan S. PHASES, a program package for the processing and analysis of diffraction data from macromolecules. Am. Crystallog. Assoc. Meet. Abstr. ser. 2. 18:1990;73.
14. Gerstein M., Lesk A. M., Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry. 33:1994;6739-6749.
15. Graves B. J., Crowther R. L., Chandran C., Rumberger J. M., Li S., Huang K.-S., Presky D. H., Familletti P. C., Wolitzky B. A., Burns D. K. Insight into E-selectin/ligand interaction from the crystal structure and mutagenesis of the lec/EGF domains. Nature. 367:1994;532-538.
16. Higashi T. The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography. J. Appl. Crystallog. 22:1989;9-18.
17. 2+-dependent-type lectins. J. Biol. Chem. 266:1991;2320-2326.
18. Koshland D. E. Jr. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl Acad. Sci. USA. 44:1958;98-104.
19. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
20. Laskowski R. A., MacArthur M. W., Moss D. S., Thorton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
21. 2+and pH. J. Biol. Chem. 263:1988;9752-9760.
22. Luzzati P. V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallog. 5:1952;802-810.
23. Matsui T., Hamako J., Suzuki M., Hayashi N., Ito M., Makita K., Fujimura Y., Ozeki Y., Titani K. Complete amino acid sequence of bitiscetin, a novel von Willebrand factor modulator protein purified from snake venom ofBitis arietans. Res. Commun. Biochem. Cell Mol. Biol. 1:1997;271-284.
24. Machius M., Wiegand G., Huber R. Crystal structure of calcium-depleted Bacilluslicheniformisα-amylase at 2.2 Å resolution. J. Mol. Biol. 246:1995;545-559.
25. Machius M., Declerck N., Huber R., Wiegand G. Activation of Bacillus licheniformisα-amylase through a disorder→order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad. Structure. 6:1998;281-292.
26. McPherson A. Crystallization. Preparation and Analysis of Protein Crystals. 1982;John Wiley & Sons, New York, Chichester, Brisbane, Toronto and Singapore. p. 82-159.
27. Mizuno H., Atoda H., Morita T. Crystallization and preliminary X-ray study of blood coagulation factor IX/factor X-binding protein with anticoagulant activity from habu snake venom. J. Mol. Biol. 220:1991;225-226.
28. Mizuno H., Fujimoto Z., Koizumi M., Kano H., Atoda H., Morita T. Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains. Nature Struct. Biol. 4:1997;438-441.
29. Morita T., Atoda H., Sekiya F. Structure and functions of coagulation factor IX/factor X-binding protein isolated from the venom ofTrimeresurus flavoviridis. Singh B. R., Tu A. T. Natural Toxins II. 1996;187-196 Plenum Press, New York.
30. Nielsen B. B., Kastrup J. S., Rasmussen H., Holtet T. L., Graversen J. H., Etzerodt M., Thøgersen H. C., Larsen I. K. Crystal structure of tetranectin, a trimeric plasminogen-binding protein with an α-helical coild coil. FEBS Letters. 412:1997;388-396.
31. Nikai T., Suzuki J., Komori Y., Ohkura M., Ohizumi Y., Sugihara H. Primary structure of the lectin from the venom of Bitis arietans (puff-adder). Biol. Pharm. Bull. 18:1995;1620-1622.
32. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Carter C. W., Sweet R. M. Methods in Enzymology. 1997;307-326 Academic Press.
33. Peng M., Lu W., Beviglia L., Niewiarowski S., Kirby E. P. Echicetin: a snake venom protein that inhibits binding of von Willebrand factor and alboaggregins to platelet glycoprotein Ib. Blood. 81:1993;2321-2328.
34. Ramakrishnan C., Ramachandran G. N. Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. Biophys. J. 5:1965;909-933.
35. Sakabe N. X-ray diffruction data collection system for modern protein crystallography with a Weissenberg camera and an imaging plate using synchrotron radiation. Nuclear Instrum. Methods Phys. Res. A. 303:1991;448-463.
36. Schlunegger M. P., Bennett M. J., Eisenberg D. Oligomer formation by 3D domain swapping: a model for protein assembly and mis assembly. Advan. Protein Chem. 50:1997;61-122.
37. Sekiya F., Yamashita T., Morita T. Role of calcium (II) ions in the recognition of coagulation factors IX and X by IX/X-bp, an anticoagulant from snake venom. Biochemistry. 34:1995;10043-10047.
38. Wang B.-C. Resolution of phase ambiguity in macromolecular crystallography. Wyckoff H. W., Hirs C. H. W., Timasheff S. N. Methods in Enzymology. 1985;90-112 Academic Press, Orlando.
39. Weis W. I., Kahn R., Fourme R., Drickamer K., Hendrickson W. A. Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. Science. 254:1991;1608-1615.
40. Weis W. I., Drickamer K., Hendrickson W. A. Structure of a C-type mannose-binding protein complexed with an oligosaccharide. Nature. 360:1992;127-134.
41. Yoshida E., Fujimura Y., Miura S., Sugimoto M., Fukui H., Narita N., Usami Y., Suzuki M., Titani K. Alboaggregin-B and botrocetin, two snake venom proteins with highly homologous amino acid sequences but totally distinct functions on von Willebrand factor binding to platelet. Biochem. Biophys. Res. Commun. 191:1993;1386-1392.
42. Zhang X.-J., Wozniak J. A., Matthews B. W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250:1995;527-552.
43. Zingali R. B., Jandrot-Perrus M., Guillin M.-C., Bon C. Bothrojaracin, a new thrombin inhibitor isolated from Bothrops jararaca venom: characterization and mechanism of thrombin inhibition. Biochemistry. 32:1993;10794-10802.