New structural motifs on the chymotrypsin fold and their potential roles in complement factor B

EMBO Journal

Volumn 19, Issue 2, 2000, Pages 164-173

  Jing, Hua ^a,b   Xu, Yuanyuan ^c   Carson, Mike ^a   Moore, Dwight ^a   Macon, Kevin J ^a,c   Volanakis, John E ^c,d   Narayana, Sthanam V L ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c The University of Alabama at Birmingham   (United States)

^d BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING   (Greece)

Author keywords

Complement system; Domain structure; Factor B; Protein protein interaction; Serine protease

Indexed keywords

ALTERNATIVE COMPLEMENT PATHWAY C3 C5 CONVERTASE; ANION; CHYMOTRYPSIN; COMPLEMENT COMPONENT C2; ENZYME PRECURSOR; SERINE PROTEINASE;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME SUBSTRATE COMPLEX; PRIORITY JOURNAL; PROTEIN FOLDING; SEQUENCE HOMOLOGY;

EID: 0034677208     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/19.2.164     Document Type: Article

References (55)

1. Arlaud, G.J., Volanakis, J.E., Thielens, N.M., Narayana, S.V.L., Rossi, V. and Xu, Y. (1998) The atypical serine proteases of the complement system. Adv. Immunol., 69, 249-307.
2. Banner, D.W., D'Arcy, A., Chene, C., Winkler, F.K., Guba, A., Konigsberg, W.H., Nemerson, Y. and Kirchhofer, D. (1996) The crystal structure of complex of blood coagulation factor VIIa with soluble tissue factor. Nature, 380, 41-46.
3. Bode, W. and Huber, R. (1992) Natural protein proteinase inhibitors and their interaction with proteinases. Eur. J. Biochem., 204, 433-451.
4. Bode, W., Brandstetter, H., Mather, T. and Stubbs, M.T. (1997) Comparative analysis of haemostatic proteinases: structural aspects of thrombin, factor Xa, factor IXa and protein C. Thromb. Haemostasis, 78, 501-511.
5. Brünger, A.T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structure. Nature, 355, 472-475.
6. Brünger, A.T. et al. (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D, 54, 905-921.
7. Carson, M. (1997) Ribbons. Methods Enzymol., 277, 493-505.
8. (Collaborative Computational Project Number 4, 1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D, 50, 760-763.
9. Chamberlain, D., Hinshelwood, J. and Perkins, S.J. (1998) The compact five-domain structure of factor B of human complement by X-ray and neutron solution scattering and homology modeling. Mol. Immunol., 35, 390.
10. Czapinska, H. and Otlewski, J. (1999) Structure and energetic determinants of the S1-site specificity in serine proteases. Eur. J. Biochem., 260, 571-595.
11. Fishelson, Z. and Müller-Eberhard, H.J. (1984) Residual hemolytic and proteolytic activity expressed by Bb after decay-dissociation of C3b, Bb. J. Immunol., 132, 1425-1429.
12. Hinshelwood, J. and Perkins, S.J. (1998) The solution structure of human factor B reveals interactions between its domains: a study by NMR and homology modeling. Mol. Immunol., 35, 389.
13. Hooft, R.W., Vriend, G., Sander, C. and Abola, E.E. (1996) Errors in protein structures. Nature, 381, 272-275.
14. Horiuchi, T., Macon, K.J., Engler, J.A. and Volanakis, J.E. (1991) Site-directed mutagenesis of the region around Cys-241 of complement component C2. J. Immunol., 147, 584-589.
15. Hourcade, D.E., Wagner L.M. and Oglesby, T.J. (1995) Analysis of the short consensus repeats of human complement factor B by site-directed mutagenesis. J. Biol. Chem., 270, 19716-19722.
16. Huber, R. and Bode, W. (1978) Structural basis of the activation and action of trypsin. J. Am. Chem. Soc., 11, 114-122.
17. Ikari, N., Hitomi, Y., Ninobe, M. and Fijii, S. (1983) Studies on esterolytic activity of alternative complement component factor B. Biochim. Biophys. Acta, 742, 318-323.
18. Jiang, F. and Kim, S.-H. (1991) 'Soft docking': matching of molecular surface cubes. J. Mol. Biol., 219, 79-102.
19. Jing, H., Babu, Y.S., Moore, D., Kilpatrick, J.M., Liu, X.-Y., Volanakis, J.E. and Narayana, S.V.L. (1998) Structures of native and complexed complement factor D: implications of the atypical His57 conformation and self-inhibitory loop in the regulation of specific serine protease activity. J. Mol. Biol., 282, 1061-1081.
20. Jing, H., Macon, K.J., Moore, D., DeLucas, L.J., Volanakis, J.E. and Narayana, S.V.L. (1999) Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D. EMBO J., 18, 804-814.
21. Jones, S. and Thornton, J.M. (1996) Principles of protein-protein interactions. Proc. Nutl Acad. Sci. USA, 93, 13-20.
22. Jones,T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A, 47, 110-119.
23. Kam, C.-M., McRae, B.J., Harper, J.W., Niemann, M.A., Volanakis, J.E. and Powers, J.C. (1987) Human complement proteins D, C2 and B. Active site mapping with peptide thioester substrates. J. Biol. Chem., 262, 3444-3451.
24. Kerr, M.A. (1980) The human complement system. Assembly of the classical pathway C3 convertase. Biochem. J., 189, 173-181.
25. Khan, A.R. and James, M.N.G. (1998) Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes. Protein Sci., 7, 815-836.
26. Kleywegt, G.J. and Brünger, A.T. (1996) Checking your imagination: applications of the free R value. Structure, 4, 897-904.
27. Kleywegt, G.J. and Jones, T.A. (1996) Efficient rebuilding of protein structures. Acta Crystallogr. D, 52, 829-832.
28. Kleywegt, G.J. and Jones, T.A. (1997) Model rebuilding and refinement practice. Methods Enzymol., 276, 208-230.
29. Kleywegt, G.J. and Read, R.J. (1997) Not your average density. Structure, 5, 1557-1569.
30. Kraut, J. (1977) Serine proteases: structure and mechanism of catalysis. Annu. Rev. Biochem., 46, 331-358.
31. Lambris, J.D. and Müller-Eberhard, H.J. (1984) Isolation and characterization of a 33,000-dalton fragment of complement factor B with catalytic and C3b binding activity. J. Biol. Chem., 259, 12685-12690.
32. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structure. J. Appl. Crystallogr., 26, 283-291.
33. Lee, J.-O., Bankston, L.A., Arnaout, M.A. and Liddington, R.C. (1995) Two conformations of the integrin A-domain (I-domain): a pathway for activation? Structure, 3, 1333-1340.
34. Liddington, R. and Bankston, L. (1998) The integrin I domain: crystals, metals and related artefacts. Structure, 6, 937-938.
35. McRee, D.E. (1992) A visual protein crystallographic software system for XII/XView. J. Mol. Graphics, 10, 44-46.
36. Navaza, J. (1994) AMoRe: an automated package for molecular replacement. Acta Crystallogr. A, 50, 157-163.
37. Nicolls, A., Sharp, K.A. and Honig, B. (1991) Protein folding and association: insights from the interfacial and thermodynamics properties of hydrocarbons. Proteins Struct. Funct. Genet., 11, 281-296.
38. Otwinowski, Z. and Minor, W. (1997) Processing X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
39. Pangburn, M.K. and Müller-Eberhard, H.J. (1986) The C3 convertase of the alternative pathway of human complement. Biochem. J., 235, 723-730.
40. Pereira, P.J.B., Berger, A., Macedo-Ribeiro, S., Huber, R., Matschiner, G., Fritz, H., Sommerhoff, C.P. and Bode, W. (1998) Human β-tryptase is a ring-like tetramer with active sites facing a central pore. Nature, 392, 306-311.
41. Perona, J.J. and Craik, C.S. (1995) Structural basis of substrate specificity in the serine proteases. Protein Sci., 4, 337-360.
42. Perona, J.J.,Tsu, C.A., McGrath, M.E., Craik, C.S. and Fletterick, R.J. (1993) Relocating a negative charge in the binding pocket of trypsin. J. Mol. Biol., 230, 934-949.
43. Read, R.J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A, 42, 140-149.
44. Sali, A. and Blundell, T.L. (1993) Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
45. Sanchez-Corral, P., Anton, L.C., Alcolea, J.M., Marques, G., Sanchez, A. and Vivanco, F. (1990) Proteolytic activity of the different fragments of factor B on the third components of complement (C3). Involvement of the N-terminal domain of Bb in magnesium binding. Mol. Immunol., 27, 891-900.
46. Smith, C.A., Vogel, C.-W. and Müller-Eberhard, H.J. (1982) Ultrastructure of cobra venom factor-dependent C3/C5 convertase and its zymogen, factor B of human complement. J. Biol. Chem., 257, 9879-9882.
47. Smith, C.A., Vogel, C.-W. and Müller-Eberhard, H.J. (1984) An electron microscopy study of the C3 convertase of human complement. J. Exp. Med., 159, 324-329.
48. Tuckwell, D.S., Xu, Y., Newham, P., Humphries, M.J. and Volanakis, J.E. (1997) Surface loops adjacent to the cation-binding site of the complement factor B-von Willebrand factor type A module determine C3b binding specificity. Biochemistry, 36, 6605-6613.
49. Ueda, A., Kearney, J.F., Roux, K.H. and Volanakis, J.E. (1987) Probing functional sites on complement protein B with monoclonal antibodies: evidence for C3b-binding sites on Ba. J. Immunol., 138, 1143-1149.
50. Volanakis, J.E. (1988) C3 convertase of complement: molecular genetics, structure and function of the catalytic domains, C2 and B. Year Immunol., 4, 218-230.
51. Volanakis, J.E. and Narayana, S.V.L. (1996) Complement factor D, a novel serine protease. Protein Sci., 5, 553-564.
52. Wang, X., Lin, X., Loy, J.A., Tang, J. and Zhang, X.C. (1998) Crystal structure of the catalytic domain of human plasmin complexed with streptokinase. Science, 281, 1662-1665.
53. Westel, R.A., Kulies, J., Lokk, M.-L., Kiepiela, P., Akama, H., Johnson, C.A.C., Densen, P. and Colten, H.R. (1996) Type II human complement C2 deficiency. Allele-specific amino acid substitutions (Ser189 to Phe, Gly444 to Arg) cause impaired C2 secretion. J. Biol. Chem., 271, 5824-5831.
54. Xu, Y. and Volanakis, J.E. (1999) C2. In Mooley, J.B. and Walport, M.J. (eds), FactsBook of Complement System, Academic Press, San Diego, CA, pp. 73-77.
55. Xu, Y., Circolo, A., Jing, H., Wang, Y., Narayana, S.V.L. and Volanakis, J.E. (2000) Mutational analysis of the primary substrate specificity pocket of complement factor B: Asp226 is a major structural determinant for P1-Arg binding. J. Biol. Chem., in press.