Crystal structure analysis of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly

Protein Science

Volumn 8, Issue 11, 1999, Pages 2355-2365

  Persson, Karina ^a,b   Schneider, Gunter ^a   Jordan, Douglas B ^c   Viitanen, Paul V ^c   Sandalova, Tatyana ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c DUPONT COMPANY   (United States)

Author keywords

Inhibitor; Macromolecular assembly; Protein crystallography; Riboflavin synthesis; Substrate analogue

Indexed keywords

LUMAZINE; PYRIMIDINE DERIVATIVE; RIBOFLAVIN; SYNTHETASE;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME STRUCTURE; FUNGUS; HYDROGEN BOND; NONHUMAN; PLANT; PRIORITY JOURNAL; STRUCTURE ANALYSIS; SYNTHESIS;

FUNGI; MAGNAPORTHE GRISEA; MIRIDAE; SPINACIA OLERACEA;

EID: 0032725195     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.11.2355     Document Type: Article

References (30)

1. Bacher A. 1990. Biosynthesis of flavin. In: F. Müller, ed. Chemistry and biochemistry of flavoproteins, Vol. I. Boca Raton, Florida: CRC Press. pp 215-259.
2. Bacher A, Baur R, Eggers U, Harders H, Otto MK, Schnepple H. 1980. Riboflavin synthase of Bacillus subtilis. Purification and properties. J Biol Chem 255:632-637.
3. Bacher A, Eberhardt S, Fischer M, Kis K, Kugelbrey K, Scheuring J, Schott K. 1997. Biosynthesis of riboflavin: Lumazine synthase and riboflavine synthase. Methods Enzymol 280:389-399.
4. Bacher A, Fischer M, Kis K, Kugelbrey K, Mörtl S, Scheuring J, Weinkauf S, Eberhardt S, Schmidt-Bäse K, Huber R, et al. 1996. Biosynthesis of riboflavin: Structure and mechanism of lumazine synthase. Biochem Soc Trans 24:89-94.
5. Brünger AT. 1992. Free R value. A novel statistical quantity to for assessing the accuracy of crystal structures. Nature 355:472-475.
6. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, et al. 1998. Crystallography & NMR systems: A new software suite for macromolecular structure determination. Acta Crystallogr D54:905-921.
7. Brünger AT, Krukowski A, Erickson JW. 1990. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr A46: 585-593.
8. (Collaborative Computational Project Number 4). 1994. The CCP4 suite. Programs for protein crystallography. Acta Crystallogr D50:760-763.
9. Cowtan KD. 1994. DM: An automated procedure for phase improvement by density modification. Joint CCP4 & ESF-EACBM Newslett Protein Crytstallog 31:34-38.
10. Engh RA, Huber R. 1991. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr D47:392-400.
11. Garcia-Ramirez J, Santos M, Revuelta J. 1995. The Saccharomyces cerivisiae RIB4 gene codes for 6,7-dimethyl-8-ribityllumazine synthase involved in riboflavin biosynthesis. Molecular characterisation of the gene and purification of the encoded protein. J Biol Chem 270:23801-23807.
12. Goldbaum FA, Polikarpov I, Cauerhff, AA, Velikovsky CA, Branden BC, Poljak RJ. 1998. Crystallization and preliminary X-ray diffraction analysis of the lumazine synthase from Brucella abortus. J Struct Biol 123:175-178.
13. Jones TA, Kjelgaard MO. 1997. Electron-density map interpretation. Methods Enzymol 277:173-207.
14. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
15. Kis K, Bacher A. 1995. Substrate channeling in the lumazine synthase/riboflavin synthase complex of Bacillus subtilis. J Biol Chem 270:16788-16795.
16. Kis K, Volk R, Bacher A. 1995. Biosynthesis of riboflavin. Studies on the reaction mechanism of 6,7-dimethyl-8-ribityllumazine synthase. Biochemistry 34:2883-2892.
17. Kleywegt GJ, Jones TA. 1997. Model building and refinement practice. Methods Enzymol 277:208-230.
18. Kraulis P. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
19. Ladenstein R, Ritsert K, Huber R, Richter G, Bacher A. 1994. The lumazine synthase/riboflavin synthase complex of Bacillus subtilis: X-ray structure analysis of hollow reconstitutes β-subunit capsids. Eur J Biochem 223: 1007-1017.
20. Ladenstein R, Schneider M, Huber R, Bartunik HD, Wilson K, Schott K, Bacher A. 1988. Heavy riboflavin synthase from Bacillus subtilis. Crystal structure analysis of the icosahedral b60 capsid at 3.3 Å resolution. J Mol Biol 203:1045-1070.
21. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291.
22. Lu G. 1996. A www service system for automatic comparison of protein structures. PDB Quarterly Newsletter 78:10-11.
23. Matthews BW. 1968. Solvent content of protein crystals. J. Mol Biol 33:491-497.
24. Merrit EA, Murphy MEP. 1994. Raster3D version 2.0 - A program photorealistic molecular graphics. Acta Crystallogr D50:869-873.
25. Mörtl S, Fischer M, Richter G, Tack J, Weinkauf S, Bacher A. 1996. Biosynthesis of riboflavin. J Biol Chem 271:33201-33207.
26. Navaza J. 1994. AMoRe: An automated package for molecular replacement. Acta Crystallogr D50:157-163
27. Otwinowski Z. 1993. Oscillation data reduction program. In: Sawyer L, Issacs N, Baily S, eds. Proceedings of the CCP4 Study Weekend: Data collection and processing. Warrington, UK: SERC Daresbury Laboratory. pp 56-62.
28. Plaut GW, Beach RL, Aogaichi T. 1970. Studies on the mechanism of elimination of protons from the methyl groups of 6,7-dimethyl-8-ribityllumazine by riboflavin synthetase. Biochemistry 9:771-785.
29. Plaut GW, Harvey RA. 1971. The enzymatic synthesis of riboflavin. Methods Enzymol 18B:515-539.
30. Ritsert K, Huber R, Turk D, Ladenstein R, Schmidt-Bäse K, Bacher A. 1995. Studies on the lumazine synthase complex of Bacillus subtilis. Crystal structure analysis of reconstituted, icosahedral β-subunit capsids with bound substrate analogue inhibitor at 2.4 Å resolution. J Mol Biol 253:151-167.