Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1′-D-ribityl) lumazine, and its analogues, riboflavin and flavin mononucleotide, at high resolution

Journal of Bacteriology

Volumn 192, Issue 1, 2010, Pages 127-133

  Sato, Yuichi ^a   Shimizu, Satoshi ^a   Ohtaki, Akashi ^a   Noguchi, Keiichi ^a   Miyatake, Hideyuki ^b   Dohmae, Naoshi ^b   Sasaki, Satoshi ^c   Odaka, Masafumi ^a   Yohda, Masafumi ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^b RIKEN   (Japan)

^c TOKYO UNIVERSITY OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

6,7 DIMETHYL 8 (1' RIBITYL)LUMAZINE; FLAVINE MONONUCLEOTIDE; GLYCINE; LUCIFERASE; LUMAZINE; PHOSPHATE; PROTEIN SUBUNIT; RIBOFLAVIN; SERINE; UNCLASSIFIED DRUG; WATER;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CHROMATOPHORE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ELECTRIC POTENTIAL; ENERGY TRANSFER; HYDROGEN BOND; LIGAND BINDING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOBACTERIUM; PHOTOBACTERIUM KISHITANII; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION;

BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; FLAVIN MONONUCLEOTIDE; LUMINESCENT PROTEINS; MOLECULAR SEQUENCE DATA; PHOTOBACTERIUM; PROTEIN BINDING; PTERIDINES; RIBOFLAVIN; X-RAY DIFFRACTION;

BACTERIA (MICROORGANISMS); PHOTOBACTERIUM 'KISHITANII CLADE';

EID: 73849130625     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01015-09     Document Type: Article

References (41)

1. Andrusier, N., R. Nussinov, and H. J. Wolfson. 2007. FireDock: fast interaction refinement in molecular docking. Proteins 69:139-159.
2. Ast, J. C., I. Cleenwerck, K. Engelbeen, H. Urbanczyk, F. L. Thompson, P. De Vos, and P. V. Dunlap. 2007. Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes. Int. J. Syst. Evol. Microbiol. 57:2073-2078.
3. Baldwin, T. O., M. L. Treat, and S. C. Daubner. 1990. Cloning and expression of the luxY gene from Vibrio fischeri strain Y-1 in Escherichia coli and complete amino acid sequence of the yellow fluorescent protein. Biochemistry 29:5509-5515.
4. Campbell, Z. T., A. Weichsel, W. R. Montfort, and T. O. Baldwin. 2009. Crystal structure of the bacterial luciferase:flavin complex provides insight into the function of the subunit. Biochemistry 48:6085-6094.
5. Chatwell, L., V. Illarionova, B. Illarionov, W. Eisenreich, R. Huber, A. Skerra, A. Bacher, and M. Fischer. 2008. Structure of lumazine protein, an optical transponder of luminescent bacteria. J. Mol. Biol. 382:44-55.
6. Collaborative Computing Project, number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50:760-763.
7. Daubner, S. C., A. M. Astorga, G. B. Leisman, and T. O. Baldwin. 1987. Yellow light emission of Vibrio fischeri strain Y-1: purification and characterization of the energy-accepting yellow fluorescent protein. Proc. Natl. Acad. Sci. U. S. A. 84:8912-8916.
8. Desjardin, D. E., A. G. Oliveira, and C. V. Stevani. 2008. Fungi bioluminescence revisited. Photochem. Photobiol. Sci. 7:170-182.
9. Emsley, P., and K. Cowtan. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60:2126-2132.
10. Fischer, M., and A. Bacher. 2008. Biosynthesis of vitamin B2: Structure and mechanism of riboflavin synthase. Arch. Biochem. Biophys. 474:252-265.
11. Fraga, H. 2008. Firefly luminescence: a historical perspective and recent developments. Photochem. Photobiol. Sci. 7:146-158.
12. Gerhardt, S., A. K. Schott, N. Kairies, M. Cushman, B. Illarionov, W. Eisenreich, A. Bacher, R. Huber, S. Steinbacher, and M. Fischer. 2002. Studies on the reaction mechanism of riboflavin synthase: X-ray crystal structure of a complex with 6-carboxyethyl-7-oxo-8-ribityllumazine. Structure 10:1371-1381.
13. Gunsalus-Miguel, A., E. A. Meighen, M. Z. Nicoli, K. H. Nealson, and J. W. Hastings. 1972. Purification and properties of bacterial luciferases. J. Biol. Chem. 247:398-404.
14. Hastings, J. W. 1996. Chemistries and colors of bioluminescent reactions: a review. Gene 173:5-11.
15. Hill, S. E., and C. S. Shoup. 1929. Observations on luminous bacteria. J. Bacteriol. 18:95-99.
16. Illarionov, B., W. Eisenreich, M. Wirth, C. Yong Lee, Y. Eun Woo, A. Bacher, and M. Fischer. 2007. Lumazine proteins from photobacteria: localization of the single ligand binding site to the N-terminal domain. Biol. Chem. 388: 1313-1323.
17. Illarionov, B., M. Fischer, C. Y. Lee, A. Bacher, and W. Eisenreich. 2004. Rapid preparation of isotopolog libraries by in vivo transformation of 1)C-glucose. Studies on 6,7-dimethyl-8-ribityllumazine, a biosynthetic precursor of vitamin B2. J. Org. Chem. 69:5588-5594.
18. Illarionov, B., V. Illarionova, J. Lee, W. van Dongen, and J. Vervoort. 1994. Expression and properties of the recombinant lumazine (riboflavin) protein from Photobacterium leiognathi. Biochim. Biophys. Acta 1201:251-258.
19. Illarionov, B., K. Kemter, S. Eberhardt, G. Richter, M. Cushman, and A. Bacher. 2001. Riboflavin synthase of Escherichia coli. Effect of single amino acid substitutions on reaction rate and ligand binding properties. J. Biol. Chem. 276:11524-11530.
20. Kita-Tsukamoto, K., M. Wada, K. Yao, A. Kamiya, S. Yoshizawa, N. Uchiyama, and K. Kogure. 2006. Rapid identification of marine bioluminescent bacteria by amplified 16S ribosomal RNA gene restriction analysis. FEMS Microbiol. Lett. 256:298-303.
21. Laskowski, R. A., J. A. Rullmannn, M. W. MacArthur, R. Kaptein, and J. M. Thornton. 1996. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8:477-486.
22. Lee, J. 1993. Lumazine protein and the excitation mechanism in bacterial bioluminescence. Biophys. Chem. 48:149-158.
23. Lee, J., D. J. O'Kane, and B. G. Gibson. 1989. Bioluminescence spectral and fluorescence dynamics study of the interaction of lumazine protein with the intermediates of bacterial luciferase bioluminescence. Biochemistry 28:4263-4271.
24. Liao, D. I., Z. Wawrzak, J. C. Calabrese, P. V. Viitanen, and D. B. Jordan. 2001. Crystal structure of riboflavin synthase. Structure 9:399-408.
25. Macheroux, P., K. U. Schmidt, P. Steinerstauch, S. Ghisla, P. Colepicolo, R. Buntic, and J. W. Hastings. 1987. Purification of the yellow fluorescent protein from Vibrio fischeri and identity of the flavin chromophore. Biochem. Biophys. Res. Commun. 146:101-106.
26. Meining, W., S. Eberhardt, A. Bacher, and R. Ladenstein. 2003. The structure of the N-terminal domain of riboflavin synthase in complex with ribo-flavin at 2.6A resolution. J. Mol. Biol. 331:1053-1063.
27. Murshudov, G. N., A. A. Vagin, and E. J. Dodson. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53:240-255.
28. O'Kane, D. J., V. A. Karle, and J. Lee. 1985. Purification of lumazine proteins from Photobacterium leiognathi and Photobacterium phosphoreum: bioluminescence properties. Biochemistry 24:1461-1467.
29. O'Kane, D. J., B. Woodward, J. Lee, and D. C. Prasher. 1991. Borrowed proteins in bacterial bioluminescence. Proc. Natl. Acad. Sci. U. S. A. 88: 1100-1104.
30. Otwinowski, Z., and W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326.
31. Petushkov, V. N., B. G. Gibson, and J. Lee. 1995. Properties of recombinant fluorescent proteins from Photobacterium leiognathi and their interaction with luciferase intermediates. Biochemistry 34:3300-3309.
32. Petushkov, V. N., M. Ketelaars, B. G. Gibson, and J. Lee. 1996. Interaction of Photobacterium leiognathi and Vibrio fischeri Y1 luciferases with fluorescent (antenna) proteins: bioluminescence effects of the aliphatic additive. Biochemistry 35:12086-12093.
33. Petushkov, V. N., and J. Lee. 1997. Purification and characterization of flavoproteins and cytochromes from the yellow bioluminescence marine bacterium Vibrio fischeri strain Y1. Eur. J. Biochem. 245:790-796.
34. Sasaki, S., T. Okamoto, and T. Fujii. 2009. Bioluminescence intensity difference observed in luminous bacteria groups with different motility. Lett. Appl. Microbiol. 48:313-317.
35. Sato, Y., and S. Sasaki. 2006. Control of the bioluminescence starting time by inoculated cell density. Anal. Sci. 22:1237-1239.
36. Sato, Y., and S. Sasaki. 2008. Observation of oscillation in bacterial luminescence. Anal. Sci. 24:423-425.
37. Schneidman-Duhovny, D., Y. Inbar, R. Nussinov, and H. J. Wolfson. 2005. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 33:W363-W367.
38. Small, E. D., P. Koka, and J. Lee. 1980. Lumazine protein from the bioluminescent bacterium Photobacterium phosphoreum. Purification and characterization. J. Biol. Chem. 255:8804-8810.
39. Truffault, V., M. Coles, T. Diercks, K. Abelmann, S. Eberhardt, H. Luttgen, A. Bacher, and H. Kessler. 2001. The solution structure of the N-terminal domain of riboflavin synthase. J. Mol. Biol. 309:949-960.
40. Tsien, R. Y. 1998. The green fluorescent protein. Annu. Rev. Biochem. 67:509-544.
41. Vagin, A., and A. Teplyakov. 1997. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30:1022-1025.