zFP538, a yellow-fluorescent protein from Zoanthus, contains a novel three-ring chromophore

Biochemistry

Volumn 44, Issue 1, 2005, Pages 202-212

  Remington, S James ^a   Wachter, Rebekka M ^a,b   Yarbrough, Daniel K ^a   Branchaud, Bruce ^a   Anderson, D C ^a   Kallio, Karen ^a   Lukyanov, Konstantin A ^c  

^a UNIVERSITY OF OREGON   (United States)

^b SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^c ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOPHORES; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; FLUORESCENCE; MASS SPECTROMETRY;

ATOMIC MODELS; CHROMOPHORE CONJUGATION; MUTANTS; THREE-RING CHROMOPHORES;

PROTEINS;

ASPARTIC ACID; GLUTAMIC ACID; GREEN FLUORESCENT PROTEIN; POLYPEPTIDE; RED FLUORESCENT PROTEIN; YELLOW FLUORESCENT PROTEIN;

ABSORPTION; ARTICLE; CHROMATOPHORE; CONJUGATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; FIELD EMISSION; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; ANIMALS; ANTHOZOA; BASE SEQUENCE; CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; DNA PRIMERS; ESCHERICHIA COLI; LUMINESCENT PROTEINS; MASS SPECTROMETRY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SOLUTIONS;

ZOANTHUS; ZOANTHUS SP.;

EID: 11844260011     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048383r     Document Type: Article

References (40)

1. Matz, M. V., Arkady, F. F., Labas, Y. A., Savitsky, A. P., Zaraisky, A. G., Markelov, M. L., and Lukyanov, S. A. (1999) Fluorescent proteins from nonbioluminescent Anthozoa species, Nat. Biotechnol. 17, 969-973.
2. Lukyanov, K. A., Fradkov, A. F., Gurskaya, N. G., Matz, M. V., Labas, Y. A., Savitsky, A. P., Markelov, M. L., Zaraisky, A. G., Zhao, X., Fang, Y., Tan, W., and Lukyanov, S. A. (2000) Natural animal coloration can be determined by a nonfluorescent green fluorescent protein homolog, J. Biol. Chem. 275, 25879-25882.
3. Dove, S., Takabayashi, M., and Hoegh-Guldberg, O. (1995) Isolation and characterization of the pink and blue pigments of Pocilloporid and Acroporid corals, Biol. Bull. 189, 288-297.
4. Dove, S. G., Hoegh-Guldberg, O., and Ranganathan, S. (2001) Major colour patterns of reef-building corals are due to a family of GFP-like proteins, Coral Reefs 19, 197-204.
5. Labas, Y. A., Gurskaya, N. G., Yanushevich, Y. G., Fradkov, A. F., Lukyanov, K. A., Lukyanov, S. A., and Matz, M. V. (2001) Diversity and evolution of the green fluorescent protein family, Proc. Natl. Acad. Sci. U.S.A. 99, 4256-4261.
6. Remington, S. J. (2002) Negotiating the speed bumps to fluorescence, Nat. Biotechnol. 20, 28-29.
7. Verkhusha, V. V., and Lukyanov, K. A. (2004) The molecular properties and applications of Anthozoa fluorescent proteins and chromoproteins, Nat. Biotechnol. 22, 289-196.
8. Bulina, M. E., Chudakov, D. M., Mudrik, N. N., and Lukyanov, K. A. (2002) Interconversion of Anthozoa GFP-like fluorescent and nonfluorescent proteins by mutagenesis, BMC Biochemistry 3.
9. Chudakov, D. M., Belousov, V. V., Zaraisky, A. G., Novoselov, V. V., Staroverov, D. B., Zorov, D. B., Lukyanov, S., and Lukyanov, K. A. (2003) Kindling fluorescent proteins for precise in vivo photolabeling, Nat. Biotechnol. 21, 191-194.
10. Chudakov, D. M., Foefanov, A. V., Mudrik, N. N., Lukyanov, S., and Lukyanov, K. A. (2003) Chromophore environment provides clue to "kindling fluorescent protein" riddle, J. Biol. Chem. 278, 7215-7219.
11. Campbell, R. E., Tour, O., Palmer, A. E., Steinbach, P. A., Baird, G. S., Zacharias, D. A., and Tsien, R. Y. (2002) A monomeric red fluorescent protein, Proc. Natl. Acad. Sci. U.S.A. 99, 7877-7882.
12. Barondeau, D. P., Putnam, C. D., Kassmann, C. J., Tainer, J. A., and Getzoff, E. D. (2003) Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures, Proc. Natl. Acad. Sci. U.S.A. 100, 12111-12116.
13. Rosenow, M. A., Huffman, H. A., Phail, M. E., and Wachter, R. M. (2004) The crystal structure of the Y66L variant of green fluorescent protein supports a cyclization-oxidation-dehydration mechanism for chromophore maturation, Biochemistry 43, 4464-4472.
14. Terskikh, A., Fradkov, A. F., Ermakova, G., Zaraisky, A. G., Tan, P., Kajava, A. V., Zhao, X., Ding, L., Lukyanov, S. A., Matz, M. V., Kim, S., Weissman, I., and Siebert, P. (2000) "Fluorescent timer": Protein that changes color with time. Science 290, 1478-1479.
15. Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K., and Tsien, R. Y. (2000) The structure of the chromophore within DsRed, a red fluorescent protein from coral, Proc. Natl. Acad. Sci. U.S.A. 87, 11990-11995.
16. Baird, G. S., Zacharias, D. A., and Tsien, R. Y. (2000) Biochemistry, mutagenesis and oligomerization of DsRed, a red fluorescent protein from coral, Proc. Natl. Acad. Sci. U.S.A. 97, 11984-11989.
17. Verkhusha, V. V., Chudakov, D. M., Gurskaya, N. G., Lukyanov, S., and Lukyanov, K. A. (2004) Common pathway for the red chromophore formation in fluorescent proteins and chromoproteins, Chem. Biol. 11, 845-854.
18. Yarbrough, D., Wachter, R. M., Kallio, K., Matz, M. V., and Remington, S. J. (2001) Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0 Å resolution, Proc. Natl. Acad. Sci. U.S.A. 98, 462-467.
19. Wall, M. A., Socolich, M., and Ranganathan, R. (2000) The structural basis for red fluorescence in the tetrameric GFP homolog DsRed, Nat. Struct. Biol. 7, 1133-1138.
20. Petersen, J., Wilmann, P. G., Beddoe, T., Oakley, A. J., Devenish, R. J., Prescott, M., and Rossjohn, J. (2003) The 2.0 Å crystal structure of eqFP611, a far-red fluorescent protein from the sea anemone Entacmaea quadricolor, J. Biol. Chem. 278, 44626-44631.
21. Prescott, M., Ling, M., Beddoe, T., Oakley, A. J., Hoegh-Guldberg, O., Devenish, R. J., and Rossjohn, J. (2003) The 2.2 Å crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation. Structure 11, 275-284.
22. Martynov, V. L., Maksimov, B. I., Matynova, N. Y., Pakhomov, A. A., Gurskaya, N. G., and Lukyanov, S. A. (2003) A purple-blue chromoprotein from Goniopora tenuidens belongs to the DsRed subfamily of GFP-like proteins, J. Biol. Chem. 278, 46288-46292.
23. Gurskaya, N. G., Savitsky, A. P., Yanushevich, Y. G., Lukyanov, S. A., and Lukyanov, K. A. (2001) Color transitions in coral's fluorescent proteins by site-directed mutagenesis, BMC Biochemists 2.
24. Zagranichny, V. E., Rudenko, N. V., Gorokhovatsky, A. Y., Zakharov, M. V., Shenkarev, Z. O., Balashova, T. A., and Arseniev, A. S. (2004) zFP538, a yellow fluorescent protein from coral, belongs to the DsRed subfamily of GFP-like proteins but possesses the unexpected site of fragmentation, Biochemistry 43, 4764-4772.
25. Leslie, A. G. W. (1996) in Cristallographic Computing (Moras, D., Podjarny, A. D., and Thierry, J. C., Eds.) pp 50-61, Oxford University Press, Oxford, U.K.
26. Evans, P. R. (1993) Data reduction, in Data Collection and Processing, Proceedings of the CCP4 Study Weekend (Sawyer, L. et al., Eds.) pp 114-122, Daresbury Laboratory, Daresbury, U.K.
27. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
28. Kissinger, C. R., Gehlhaar, D. K., and Fogel, D. B. (1999) Rapid automated molecular replacement by evolutionary search, Acta Crystallogr., Sect. D 55, 484-491.
29. Tronrud, D. E., Ten Eyck, L. F., and Matthews, B. W. (1987) An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallogr., Sect. A 43, 489-503.
30. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr., Sect. A 47, 110-119.
31. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR Systems: A new software suite for macromolecular structure determination, Acta Crystallogr., Sect. D 54, 905-921.
32. Brunger, A. T. (1997) Free R value: Cross-validation in crystallography, Methods Enzymol. 277, 366-396.
33. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
34. Schwede, T. F., Retey, J., and Schulz, G. E. (1999) Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile, Biochemistry 38, 5355-5361.
35. Ormo, M., Cubitt, A. B., Kallio, K., Gross, L. A., Tsien, R. Y., and Remington, S. J. (1996) Crystal structure of the Aequorea victoria green fluorescent protein, Science 273, 1392-1395.
36. Wachter, R. M., Elsliger, M. A., Kallio, K., Hanson, G. T., and Remington, S. J. (1998) Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein, Structure 6, 1267-1277.
37. Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H., and Miyawaki, A. (2002) An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein, Proc. Natl. Acad. Sci. U.S.A. 99, 12651-12656.
38. Gurskaya, N. G., Fradkov, A. F., Terskikh, A., Matz, M. V., Labas, Y. A., Martynov, V. I., Yanushevich, Y. G., Lukyanov, K. A., and Lukyanov, S. A. (2001) GFP-like chromoproteins as a source of far-red fluorescent proteins, FEBS Lett. 507, 16-20.
39. Dao-pin, S., Anderson, D. F., Baase, W. A., Dahlquist, F. W., and Matthews, B. W. (1991) The structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme, Biochemistry 30, 11521-11529.
40. Fradkov, A. F., Chen, Y., Ding, L., Barsova, E. V., Matz, M. V., and Lukyanov, S. A. (2000) Novel fluorescent protein from Discosoma coral and its mutants possesses a unique far-red fluorescence, FEBS Lett. 479, 127-130.