Sequence Determinants of Quaternary Structure in Lumazine Synthase

Molecular Biology and Evolution

Volumn 21, Issue 1, 2004, Pages 97-107

  Fornasari, María Silvina ^a   Laplagne, Diego A ^b   Frankel, Nicolás ^c   Cauerhff, Ana A ^b   Goldbaum, Fernando A ^b   Echave, Julián ^a  

^a UNIVERSIDAD NACIONAL DE QUILMES   (Argentina)

^b UNIVERSIDAD DE BUENOS AIRES   (Argentina)

^c INSTITUTO DE FISIOLOGÍA   (Argentina)

Author keywords

Evolutionary rates; Lumazine synthase; Quaternary structure; Structuralconstraints

Indexed keywords

LUMAZINE; LUMAZINE SYNTHASE; SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ENZYME SUBUNIT; EVOLUTION; FUNGUS; MICROORGANISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT; PROTEIN ASSEMBLY; PROTEIN QUATERNARY STRUCTURE; STRUCTURE ANALYSIS;

BASE SEQUENCE; CLUSTER ANALYSIS; DATABASES, GENETIC; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIENZYME COMPLEXES; PHYLOGENY; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; SEQUENCE ALIGNMENT;

FUNGI; MIRIDAE;

EID: 1242329482     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg244     Document Type: Article

References (48)

1. Adachi, J., and M. Hasegawa. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:459-468.
2. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Atchley, W. R., W. Terhalle, and A. Dress. 1999. Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48:501-516.
4. Bacher, A., R. Baur, U. Eggers, H. D. Harders, M. K. Otto, and H. Schnepple. 1980. Riboflavin synthases of Bacillus subtilis. Purification and properties. J. Biol. Chem. 255: 632-637.
5. Bacher, A. 1986. Heavy riboflavin synthase from Bacillus subtilis. Methods Enzymol. 122:192-199.
6. Bacher, A., M. Fischer, K. Kis, K. Kugelbrey et al. (13 co-authors). 1996. Biosynthesis of riboflavin: structure and mechanism of lumazine synthase. Biochem. Soc. Trans. 24: 89-94.
7. Bacher, A., S. Eberhardt, W. Eisenreich, M. Fischer, S. Herz, B. Illarionov, K. Kis, and G. Richter. 2001. Biosynthesis of riboflavin. Vitam. Horm. 61:1-49.
8. Baldi, P. C., C. A. Velikovsky, B. C. Braden, G. H. Giambartolomei, C. A. Fossati, and F. A. Goldbaum. 2000. Structural, functional and immunological studies on a polymeric bacterial protein. Braz. J. Med. Biol. Res. 33:741-747.
9. Braden, B. C., C. A. Velikovsky, A. A. Cauerhff, I. Polikarpov, and F. A. Goldbaum. 2000. Divergence in macromolecular assembly: x-ray crystallographic structure analysis of lumazine synthase from Brucella abortus. J. Mol. Biol. 297:1031-1036.
10. Casari, G., C. Sander, and A. Valencia. 1995. A method to predict functional residues in proteins. Nat. Struct. Biol. 2: 171-178.
11. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
12. Gerhardt, S., I. Haase, S. Steinbacher, J. T. Kaiser, M. Cushman, A. Bacher, R. Huber, and M. Fischer. 2002. The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase. J. Mol. Biol. 318: 1317-1329.
13. Goldbaum, F. A., C. A. Velikovsky, P. C. Baldi, S. Mörtl, A. Bacher, and C. A. Fossati. 1999. The 18-kDa cytoplasmic protein of Brucella species-an antigen useful for diagnosis-is a lumazine synthase. J. Med. Microbiol. 48:833-839.
14. Golding, G. B., and A. M. Dean. 1998. The structural basis of molecular adaptation. Mol. Biol. Evol. 15:355-369.
15. Gu, X., and J. Zhang. 1997. A simple method for estimating the parameter of substitution rate variation among sites. Mol. Biol. Evol. 14:1106-1113.
16. Gu, X. 1999. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16:1664-1674.
17. Gu, X. 2001. Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18:453-464.
18. Gu, X., and K. Vander Velden. 2002. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18:500-501.
19. Guex, N., A. Diemand, and M. C. Peitsch. 1999, Protein modelling for all. Trends Biochem. Sci. 24:364-367.
20. Henrick, K., and J. M. Thornton. 1998, PQS: a protein quaternary structure file server, Trends Biochem. Sci. 23:358-361.
21. Huang, X., H. M. Holden, and F. M. Raushel. 2001. Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu. Rev. Biochem. 70:149-180.
22. Jordan, D. B., K. O. Bacot, T. J. Carlson, M. Kessel, and P. V. Viitanen. 1999. Plant riboflavin biosynthesis. Cloning, chloroplast localization, expression, purification, and partial characterization of spinach lumazine synthase. J. Biol. Chem. 274:22114-22121.
23. Karshikoff, A., and R. Ladenstein. 2001. Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads. Trends Biochem. Sci. 26:550-556.
24. Kearney, E. B., J. Goldenberg, J. Lipsick, and M. Perl. 1979. Flavokinase and FAD synthetase from Bacillus subtilis specific for reduced flavins. J. Biol. Chem. 254:9551-9557.
25. Kis, K., R. Volk, and A. Bacher. 1995. Biosynthesis of riboflavin. Studies on the reaction mechanism of 6,7-dimethyl-8-ribityllumazine synthase. Biochemistry 34:2883-2892.
26. Kis, K., and A. Bacher. 1995. Substrate channeling in the lumazine synthase/riboflavin synthase complex of Bacillus subtilis. J. Biol. Chem. 270:16788-16795.
27. Ladenstein, R., H. C. Ludwig, and A. Bacher. 1983. Crystallization and preliminary X-ray diffraction study of heavy riboflavin synthase from Bacillus subtilis. J. Biol. Chem. 258:11981-11983.
28. Ladenstein, R., M. Schneider, R. Huber, H. D. Bartunik, K. Wilson, K. Schott, and A. Bacher. 1988. Heavy riboflavin synthase from Bacillus subtilis. Crystal structure analysis of the icosahedral beta 60 capsid at 3.3 A resolution. J. Mol. Biol. 203:1045-1070.
29. Ladenstein, R., K. Ritsert, R. Huber, G. Richter, and A. Bacher. 1994. The lumazine synthase/riboflavin synthase complex of Bacillus subtilis. X-ray structure analysis of hollow reconstituted beta-subunit capsids. Eur. J. Biochem. 223:1007-1017.
30. Landgraf, R., D. Fischer, and D. Eisenberg. 1999. Analysis of heregulin symmetry by weighted evolutionary tracing. Protein Eng. 12:943-951.
31. Larson, S. M., I. Ruczinski, A. R. Davidson, D. Baker, and K. W. Plaxco. 2002. Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. J. Mol. Biol. 316:225-233.
32. Liao, D. I., Z. Wawrzak, J. C. Calabrese, P. V. Viitanen, and D. B. Jordan. 2001. Crystal structure of riboflavin synthase. Structure (Camb.) 9:399-408.
33. Meining, W., S. Mörtl, M. Fischer, M. Cushman, A. Bacher, and R. Ladenstein. 2000. The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate intermediate analogue. J. Mol. Biol. 299:181-197.
34. Mörtl, S., M. Fischer, G. Richter, J. Tack, S. Weinkauf, and A. Bacher. 1996. Biosynthesis of riboflavin. Lumazine synthase of Escherichia coli. J. Biol. Chem. 271:33201-33207.
35. Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
36. Page, R. D. 1996. Tree View: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357-358.
37. Persson, K., G. Schneider, D. B. Jordan, P. V. Viitanen, and T. Sandalova. 1999. Crystal structure analysis of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly. Protein Sci. 8:2355-2365.
38. Ptitsyn, O. B. 1998. Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes? J. Mol. Biol. 278:655-666.
39. -. 1999. Protein evolution and protein folding: non-functional conserved residues and their probable role. Pacific Symposium on Biocomputing, Hawaii, January 4-9;494-504.
40. Ritsert, K., R. Huber, D. Turk, R. Ladenstein, K. Schmidt-Bäse, and A. Bacher. 1995. Studies on the lumazine synthase/riboflavin synthase complex of Bacillus subtilis: crystal structure analysis of reconstituted, icosahedral beta-subunit capsids with bound substrate analogue inhibitor at 2.4 A resolution. J. Mol. Biol. 253:151-167.
41. Roulston, M. S. 1999. Estimating the errors on measured entropy and mutual information. Physica D 125:285-294.
42. Schott, K., R. Ladenstein, A. Konig, and A. Bacher. 1990. The lumazine synthase-riboflavin synthase complex of Bacillus subtilis. Crystallization of reconstituted icosahedral beta-subunit capsids. J. Biol. Chem. 265:12686-12689.
43. Shenkin, P. S., B. Erman, and L. D. Mastrandrea. 1991. Information-theoretical entropy as a measure of sequence variability. Proteins 11:297-313.
44. Sobolev, V., A. Sorokine, J. Prilusky, E. E. Abola, and M. Edelman. 1999. Automated analysis of interatomic contacts in proteins. Bioinformatics 15:327-332.
45. Spiegel, M. R. 1998. Statistics. McGraw-Hill-Education, Europe.
46. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
47. Westhead, D. R., D. C. Hatton, and J. M. Thornton, 1998. An atlas of protein topology cartoons available on the World-Wide Web. Trends Biochem. Sci. 23:35-36.
48. Zhang, X., W. Meining, M. Fischer, A. Bacher, and R. Ladenstein. 2001. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons. J. Mol. Biol. 306:1099-1114.