Evolutionary conserved rigid module-domain interactions can be detected at the sequence level: The examples of complement and blood coagulation proteases

Journal of Molecular Biology

Volumn 282, Issue 2, 1998, Pages 459-470

  Gaboriaud, Christine ^a   Rossi, Véronique ^b,c   Fontecilla Camps, Juan Carlos ^a   Arlaud, Gérard J ^b  

^a Lab Cristallogenese Cristal P   (France)

^b INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^c UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

Author keywords

Blood coagulation; Complement; Domain domain interaction; Protein module; Sequence homology

Indexed keywords

BLOOD CLOTTING FACTOR; COMPLEMENT; EPIDERMAL GROWTH FACTOR; PROTEIN C; PROTEINASE;

ARTICLE; BLOOD CLOTTING; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; GENE CLUSTER; GENETIC CONSERVATION; HUMAN; LIMULUS; NONHUMAN; PRIORITY JOURNAL;

EID: 0032544301     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2008     Document Type: Article

References (48)

1. Appel, R. D., Bairoch, A. & Hochstrasser, D. F. (1994). A new generation of information retrieval tools for biologists: the example of the ExPASY server. Trends Biochem. Sci. 19, 258-260.
2. Arlaud, G. J. & Gagnon, J. (1981). C1r and C1 s subcomponents of human complement: two serine proteinases lacking the "histidine-loop" disulphide bridge. Biosci. Rep. 1, 779-784.
3. Arlaud, G. J. & Thielens, N. M. (1993). Human complement serine proteases C1 r and C1 s and their proenzymes. Methods Enzymol. 223, 61-82.
4. Arlaud, G. J., Colomb, M. G. & Gagnon, J. (1987). A functional model of the human C1 complex. Immunol. Today, 8, 106-111.
5. Arlaud, G. J., Volanakis, J. E., Thielens, N. M., Narayana, S. V. L., Rossi, V. & Xu, Y. (1998). The atypical serine proteases of the complement system. Advan. Immunol. 69, 249-307.
6. Banner, D. W. (1997). The factor VIIa/tissue factor complex. Thromb. Haemost. 78, 512-515.
7. Banner, D. W., D'Arcy, A., Chene, C., Winkler, F. K., Guha, A., Konigsberg, W. H., Nemerson, Y. & Kirchhofer, D. (1996). The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature, 380, 41-46.
8. Barlow, P. N., Steinkasserer, A., Baron, M., Day, A. J., Sim, R. B. & Campbell, I. D. (1993). Solution structure of a pair of complement modules by nuclear magnetic resonance. J. Mol. Biol. 232, 268-284.
9. Benner, S. A. (1989). Patterns of divergence in homologous proteins as indicators of tertiary and quaternary structures. Advan. Enzyme Regul. 28, 219-236.
10. Benner, S. A. (1992). Predicting de novo the folded structure of proteins. Curr. Opin. Struct. Biol. 2, 402-412.
11. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
12. Bode, W., Brandstetter, H., Mather, T. & Stubbs, M. T. (1997). Comparative analysis of haemostatic proteinases: structural aspects of thrombin, factor Xa, factor IXa and protein C. Thromb. Haemost. 78, 501-511.
13. Bork, P. & Bairoch, A. (1995). Extracellular protein modules: a proposed nomenclature. Trends Biochem. Sci. 20, (Suppl.), C03.
14. Bork, P. & Beckmann, G. (1993). The CUB domain. A widespread module in developmentally regulated proteins. J. Mol. Biol. 231, 539-545.
15. Bork, P., Downing, A. K., Kieffer, B. & Campbell, I. D. (1996). Structure and distribution of modules in extracellular proteins. Quart. Rev. Biophys. 29, 119-167.
16. Brandstetter, H., Bauer, M., Huber, R., Lollar, P. & Bode, W. (1995). X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia b. Proc. Natl Acad. Sci. USA, 92, 9796-9800.
17. Brenner, S. (1988). The molecular evolution of genes and proteins: a tale of two serines. Nature, 334, 528-530.
18. Casari, G., Sander, C. & Valencia, A. (1995). A method to predict functional residues in proteins. Nature Struct. Biol. 2, 171-178.
19. +-induced allosteric regulation of catalytic activity in serine proteases. Proc. Natl Acad. Sci. USA, 93, 10653-10656.
20. Dickinson, C. D., Kelly, C. R. & Ruf, W. (1996). Identification of surface residues mediating tissue factor binding and catalytic function of the serine proteases factor VIIa. Proc. Natl Acad. Sci. USA, 93, 14379-14384.
21. Doolittle, R. F. (1995). The multiplicity of domain in proteins. Annu. Rev. Biochem. 64, 287-314.
22. Endo, Y., Sato, T., Matsushita, M. & Fujita, T. (1996). Exon structure of the gene encoding the human mannose-binding proteins-associated serine protease (MASP) light chain: comparison with complement C1r and C1s genes. Int. Immunol. 8, 1355-1358.
23. Hegyi, H. & Bork, P. (1997). On the classification and evolution of protein modules. J. Protein Chem. 16, 545-551.
24. Higashi, S., Matsumoto, N. & Iwanaga, S. (1996). Molecular mechanism of tissue factor-mediated acceleration of factor VIIa activity. J. Biol. Chem. 271, 26569-26574.
25. Ji, X., Azumi, K., Sasaki, M. & Nonaka, M. (1997). Ancient origin of the complement lectin pathway revealed by molecular cloning of mannan binding protein-associated serine protease from a urochordate, the Japanese ascidian, Halocynthia roretzi. Proc. Natl Acad. Sci. USA, 94, 6340-6345.
26. Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of proteins structures. J. Appl. Crystallog. 24, 946-950.
27. Kurosky, A., Barnett, D. R., Lee, T.-H., Touchstone, B., Hay, R. E., Arnott, M. S., Bowman, B. H. & Fitch, W. M. (1980). Covalent structure of human haptoglobin: a serine protease homolog. Proc. Natl Acad. Sci. USA, 77, 3388-3392.
28. Lacroix, M., Rossi, V., Gaboriaud, C., Chevallier, S., Jaquinod, M., Thielens, N. M., Gagnon, J. & Arlaud, G. J. (1997). Structure and assembly of the catalytic regions of human complement protease C1r: a three-dimensional model based on chemical cross-linking and homology modeling. Biochemistry, 36, 6270-6282.
29. Mather, T., Oganessyan, V., Hof, P., Huber, R., Foundling, S., Esmon, C. & Bode, W. (1996). The 2.8 Å crystal structure of Gla-domainless activated protein C. EMBO. J. 15, 6822-6831.
30. Matsushita, M. & Fujita, T. (1992). Activation of the classical complement pathway by mannose-binding proteins in association with a novel C1s-like serine protease. J. Exp. Med. 17, 1497-1502.
31. Muta, T., Miyata, T., Misumi, Y., Tokunaga, F., Nakamura, T., Toh, Y., Ikehara, Y. & Iwanaga, S. (1991). Limulus factor C. An endotoxin-sensitive serine protease zymogen with a mosaic structure of complement-like, epidermal growth factor-like, and lectin-like domains. J. Biol. Chem. 26, 6554-6561.
32. Neurath, H. (1984). Evolution of proteolytic enzymes. Science, 224, 350-357.
33. Padmanabhan, K., Padmanabhan, K. P., Tulinsky, A., Park, C. H., Bode, W., Huber, R., Blankenship, D. T., Cardin, A. D. & Kisiel, W. (1993). Structure of human Des(1-45) factor Xa at 2.2 Å resolution. J. Mol. Biol. 232, 947-966.
34. Patthy, L. (1993). Modular design of proteases of coagulation, fibrinolysis and complement activation: implications for protein engineering and structure-function studies. Methods Enzymol. 223, 10-21.
35. Patthy, L. (1994). Introns and exons. Curr. Opin. Struct. Biol. 4, 383-392.
36. Pazos, F., Helmer-Citterich, M., Ausiello, G. & Valencia, A. (1997). Correlation mutations contain information about protein-proteins interaction. J. Mol. Biol. 271, 511-523.
37. Rossi, V., Gaboriaud, C., Lacroix, M., Ulrich, J., Fontecilla-Camps, J.-C., Gagnon, J. & Arlaud, G. J. (1995). Structure of the catalytic region of human complement protease C1s: study by chemical cross-linking and three-dimensional homology modeling. Biochemistry, 34, 7311-7321.
38. Rossi, V., Bally, I., Thielens, N. M., Esser, A. F. & Arlaud, G. J. (1998). Baculovirus-mediated expression of truncated modular fragments from the catalytic region of human complement serine proteases C1s. Evidence for the involvement of both complement control protein modules in the recognition of the C4 protein substrate. J. Biol. Chem. 273, 1232-1239.
39. Sander, C. & Schneider, R. (1991). Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Struct. Funct. Genet. 9, 56-68.
40. Sato, T., Endo, Y., Matsushita, M. & Fujita, T. (1994). Molecular characterization of a novel serine protease involved in activation of the complement system by mannose-binding protein. Int. Immunol. 6, 665-669.
41. Smith, A. B., Esko, J. D. & Hajduk, S. L. (1995). Killing of trypanosomes by the human haptoglobin-related protein. Science, 268, 284-286.
42. Sonnhammer, E. L., Eddy, S. R. & Durbin, R. (1997). Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins: Struct. Funct. Genet. 28, 405-420.
43. Spitzfaden, C., Grant, R. P., Mardon, H. J. & Campbell, I. D. (1997). Module-module interactions in the cell binding region of fibronectin: stability, flexibility and specificity. J. Mol. Biol. 265, 565-579.
44. Thiel, S., Vorup-Jensen, T., Stover, C. M., Schwaeble, W., Laursen, S. B., Poulsen, K., Willis, A. C., Eggleton, P., Hansen, S., Holmskov, U., Reid, K. B. M. & Jensenius, J. C. (1997). A second serine protease associated with mannan-binding lectin that activates complement. Nature, 386, 506-510.
45. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22, 4673-4680.
46. Tosi, M., Duponchel, C., Meo, T. & Couture-Tosi, E. (1989). Complement genes C1r and C1s feature an intronless serine protease domain closely related to haptoglobin. J. Mol. Biol. 208, 709-714.
47. Urushibara, N., Kumazaki, T. & Ishii, S. (1992). Hemoglobin-binding site on human haptoglobin. Identification of lysyl residues participating in the binding. J. Biol. Chem. 267, 13413-13417.
48. Wiles, A. P., Shaw, G., Bright, J., Perczel, A., Campbell, I. D. & Barlow, P. N. (1997). NMR studies of a viral protein that mimics the regulators of complement activation. J. Mol. Biol. 272, 253-265.