Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis

Journal of Biochemistry

Volumn 119, Issue 1, 1996, Pages 49-57

  Kumasaka, Takashi ^a,b   Yamamoto, Masaki ^b   Moriyama, Hideaki ^a   Tanaka, Nobuo ^a   Sato, Mamoru ^c   Katsube, Yukiteru ^c   Yamakawa, Yoshio ^d   Omori Satoh, Tamotsu ^d   Iwanaga, Sadaaki ^e   Ueki, Tatzuo ^b  

^a Tokyo Institute of Technology ^*  (Japan)

^b INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^c OSAKA UNIVERSITY   (Japan)

^d NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

^e KYUSHU UNIVERSITY   (Japan)

Author keywords

Crystal structure; Snake venom; Zinc protease

Indexed keywords

DISULFIDE; HISTIDINE; METHIONINE; PROTEINASE; SNAKE VENOM; ZINC; CROTALUS ADAMANTEUS PROTEINASE II; H(2) PROTEINASE; H(2)-PROTEINASE; METALLOPROTEINASE;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DISULFIDE BOND; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME PURIFICATION; ENZYME STRUCTURE; NONHUMAN; PROTEIN DOMAIN; SNAKE; AMINO ACID SEQUENCE; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; ENZYME SPECIFICITY; ENZYMOLOGY; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; CROTALID VENOMS; CRYSTALLOGRAPHY, X-RAY; DISULFIDES; METALLOENDOPEPTIDASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY; TRIMERESURUS; ZINC;

ANIMALIA; CROTALUS ADAMANTEUS; SERPENTES; TRIMERESURUS FLAVOVIRIDIS;

EID: 0029671268     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a021215     Document Type: Article

References (41)

1. Hooper, N.M. (1994) Families of zinc metalloproteases. FEBS Lett. 354, 1-6
2. Bode, W., Gomis-Rüth, F.X., and Stöcker, W. (1993) Astacins, serralysins, snake venom and matrix metalloproteinases exhibit identical zinc-binding environments (HEXXHXXGXXH and Met-turn) and topologies and should be grouped into a common family, the 'metzincins.' FEBS Lett. 331, 134 140
3. Stöcker, W., Grams, F., Baumann, U., Reinemer, P., Gomis-Rüth, F.-X., McKay, D.B., and Bode, W. (1995) The metzincins Topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases. Prot. Sci. 4, 823-840
4. Gomis-Rüth, F.X., Stöcker, W., Huber, R., Zwilling, R., and Bode, W. (1994) Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. J. Mol. Biol. 229, 945-968
5. Gomis-Rüth, F.X., Kress, L.F., and Bode, W. (1993) First structure of a snake venom metalloproteinase: A prototype for matrix metalloproteinases/collagenases. EMBO J. 12, 4151-4157
6. Gomis-Rüth, F.X., Kress, L.F., Kellermann, J., Mayr, I., Lee, X., Huber, R., and Bode, W. (1994) Refined 2.0 A X-ray crystal structure of the snake venom zinc-endopeptidase adamalysin II. J. Mol. Biol. 239, 513-544
7. Zhang, D., Botos, I., Gomis-Rüth, F.X., Doll, R., Blood, C., Njoroge, F.G., Fox, J.W., Bode, W., and Meyer, E.F. (1994) Structural interaction of natural and synthetic inhibitors with the venom metalloproteinase, atrolysin C (form d). Proc. Natl. Acad. Sci. USA 91, 8447-8451
8. Lovejoy, B., Cleasby, A., Hassell, A.M., Longley, K., Luther, M.A., Weigl, D., McGeehan, G., McElroy, A.B., Drewry, D., Lambert, M.H., and Jordan, S.R. (1994) Structures of the catalytic domain of fibroblast collaganase complexed with an inhibitor. Science 263, 375-377
9. Lovejoy, B., Hassell, A.M., Luther, M.A., Weigl, D., and Jordan, S.R. (1994) Crystal structures of recombinant 19-kDa human fibroblast collaganase complexed to itself. Biochemistry 33, 8207-8217
10. Borkakoti, N., Winkler, F.K., Williams, D.H., D'Arcy, A., Broadhurst, M.J., Brown, P.A., Johnson, W.H., and Murray, E. J. (1994) Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor. Nature Struct. Biol. 1, 106-110
11. Stams, T., Spurlino, J.C., Smith, D.L., Wahl, R.C., Ho, T.F., Qoronfleh, M.W., Banks, T.M., and Rubin, B. (1994) Structure of human neutrophil collagenase reveals large S1′ specificity pocket. Nature Struct. Biol. 1, 119-123
12. Gooley, P.R., O'Connell, J.F., Marcy, A.I., Cuca, G.C., Salowe, S.P., Bush, B.L., Hermes, J.D., Esser, C.K., Hagmann, W.K., Spinger, J.P., and Johnson, B.A. (1994) The NMR structure of the inhibited catalytic domain of human stromelysin-1. Nature Struct. Biol. 1, 111-118
13. Baumann, U., Wu, S., Flaherty, K.M., and McKay, D.B. (1993) Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: A two-domain protein with a calcium binding parallel beta roll motif. EMBO J. 12, 3357-3364
14. Baumann, U. (1994) Crystal structure of the 50 kDa metallo protease from Serratia marcescens. J. Mol. Biol. 242, 244-251
15. Ohsaka, A., Just, M., and Habermann, E. (1973) Action of snake venom hemorrhagic principles on isolated glomerular basement membrane. Biochim. Biophys. Acta 323, 415-428
16. Iwanaga, S. and Takeya, H. (1993) Structure and function of snake venom metalloproteinase family in Methods in Protein Sequence Analysis (Imahori, K. and Sakiyama, F., eds.) pp. 107 115, Plenum Press, New York
17. Takahashi, T. and Ohsaka, A. (1970) Purification and characterization of a proteinase in the venom of Trimeresurus flavoviridis. Biochim. Biophys. Acta 198, 293-307
18. 2-proteinase, a nonhemorrhagic metalloproteinase, isolated from the habu snake, Trimeresurus flavoviridis. J. Biochem. 106, 151-157
19. Takeya, H., Nishida, S., Nishino, N., Makinose, Y., Omori-Satoh, T., Nikai, T., Sugihara, H., and Iwanaga, S. (1993) Primary structures of platelet aggregation inhibitors (disintegrins) autoproteolytically released from snake venom hemorrhagic metalloproteinases and new fluorogenic peptide substrates for these enzymes. J. Biochem. 113, 473-483
20. Omori-Satoh, T. (1977) Antihemorrhagic factor as a proteinase inhibitor isolated from the serum of Trimeresurus flavoviridis. Biochim. Biophys. Acta 495, 93-98
21. Takeya, H., Oda, K., Miyata, T., Omori-Satoh, T., and Iwanaga, S. (1990) The complete amino acid sequence of the high molecular mass hemorrhagic protein HR1B isolated from the venom of Trimeresurus flavoviridis. J. Biol. Chem. 265, 16068-16073
22. Takahashi, T. and Ohsaka, A. (1969) Purification and some properties of two hemorrhagic principles (HR2a and HR2b) in the venom of Trimeresurus flavoviridis; complete separation of the principles from proteolytic activity. Biochim. Biophys. Acta 207, 65-75
23. Miyata, T., Takeya, H., Ozeki, Y., Arakawa, M., Tokunaga, F., Iwanaga, S., and Omori-Satoh, T. (1989) Primary structures of hemorrhagic protein, HR2a, isolated from the venom of Trimeresurus flavoviridis. J. Biochem. 105, 847-853
24. 2-proteinase from the venom of Trimeresurus flavoviridis. J. Biochem. 177, 929-930
25. Sato, M., Yamamoto, M., Imada, K., Katsube, Y., Tanaka, N., and Higashi, T. (1991) Development of a high-speed data-collection system with an imaging plate in consideration of large-unit-cell crystals. J. Appl. Cryst. 23, 348-357
26. Higashi, T. (1990) Auto-indexing of oscillation images. J. Appl. Cryst. 23, 253-257
27. Sakabe, N. (1991) X-ray diffraction collection system for modern protein crystallography with a Weissenberg camera and an imaging plate using synchrotron radiation. Nucl. Instrum. Methods. Phys. Res. A303, 448-463
28. Higashi, T. (1989) The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography. J. Appl. Cryst. 22, 9-18
29. Collaborative Computational Project, Number 4 (1994) The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763
30. Furey, W. and Swaminathan, S. (1990) PHASES-A program package for the processing and analysis of diffraction data from macromolecules. Am. Crystallogr. Assoc. Annu. Mtg. Program Abst. 18, 73
31. Bio-Graphics (1994) Turbo-FRODO (version 5.02), Manual
32. Brünger, A.T. (1992) X-PLOR (version 3.0), Manual
33. Engh, R.A. and Huber, R. (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst. A47, 392-400
34. Ramakrishnan, C. and Ramachandran, G.N. (1965) Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. Biophys. J. 5, 909-933
35. Luzzati, P.V. (1952) Traitement statistique des erreurs dans la determination des structures cristallines. Acta. Cryst. 5, 802
36. Schechter, I. and Berger, A. (1967) On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. Commun. 27, 157-162
37. Hakånsson, K., Wehnert, A., and Liljas, A. (1994) X-ray analysis of metal-substituted human carbonic anhydrase II derivatives. Acta Cryst. D50, 93-100
38. Gomis-Rüth, F.-X., Grams, F., Yiallouros, I., Nar, H., Küsthardt, U., Zwilling, R., Bode, W., and Stöcker, W. (1994) Crystal structures, spectroscopic features, and catalytic properties of cobalt(II), copper(II), nickel(II), and mercury(II) derivatives of the zinc endopeptidase astacin. J. Biol. Chem. 269, 17111-17117
39. Hite, L., Jia, L.-G., Bjanason, J.B., and Fox, J.W. (1994) cDNA sequences for four snake venom metalloproteinases: Structure, classification, and their relationship to mammalian reproductive proteins. Arch. Biochim. Biophys. 308, 182-191
40. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950
41. Au, L.C., Huang, Y.B., Huang, T.F., Teh, G.W., Lin, H.H., and Choo, K.B. (1991) A common precursor for a putative hemorrhagic protein and rhodostomin, a platelet aggregation inhibitor of the venom of Calloselasma rhodostoma: Molecular cloning and sequence analysis. Biochem. Biophys. Res. Commun. 181, 585-593