Skip to main content
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 2000 Nov;9(11):2085–2093. doi: 10.1110/ps.9.11.2085

Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure.

Z J Liu 1, E S Vysotski 1, C J Chen 1, J P Rose 1, J Lee 1, B C Wang 1
PMCID: PMC2144499  PMID: 11152120

Abstract

The crystal structure of the photoprotein obelin (22.2 kDa) from Obelia longissima has been determined and refined to 1.7 A resolution. Contrary to the prediction of a peroxide, the noncovalently bound substrate, coelenterazine, has only a single oxygen atom bound at the C2-position. The protein-coelenterazine 2-oxy complex observed in the crystals is photo-active because, in the presence of calcium ion, bioluminescence emission within the crystal is observed. This structure represents only the second de novo protein structure determined using the anomalous scattering signal of the sulfur substructure in the crystal. The method used here is theoretically different from that used for crambin in 1981 (4.72 kDa) and represents a significant advancement in protein crystal structure determination.

Full Text

The Full Text of this article is available as a PDF (4.9 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur J Biochem. 1977 Nov 1;80(2):319–324. doi: 10.1111/j.1432-1033.1977.tb11885.x. [DOI] [PubMed] [Google Scholar]
  2. Brünger 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. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905–921. doi: 10.1107/s0907444998003254. [DOI] [PubMed] [Google Scholar]
  3. Charbonneau H., Walsh K. A., McCann R. O., Prendergast F. G., Cormier M. J., Vanaman T. C. Amino acid sequence of the calcium-dependent photoprotein aequorin. Biochemistry. 1985 Nov 19;24(24):6762–6771. doi: 10.1021/bi00345a006. [DOI] [PubMed] [Google Scholar]
  4. Conti E., Franks N. P., Brick P. Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure. 1996 Mar 15;4(3):287–298. doi: 10.1016/s0969-2126(96)00033-0. [DOI] [PubMed] [Google Scholar]
  5. Dauter Z., Dauter M., de La Fortelle E., Bricogne G., Sheldrick G. M. Can anomalous signal of sulfur become a tool for solving protein crystal structures? J Mol Biol. 1999 May 28;289(1):83–92. doi: 10.1006/jmbi.1999.2743. [DOI] [PubMed] [Google Scholar]
  6. Derewenda Z., Yariv J., Helliwell J. R., Kalb A. J., Dodson E. J., Papiz M. Z., Wan T., Campbell J. The structure of the saccharide-binding site of concanavalin A. EMBO J. 1989 Aug;8(8):2189–2193. doi: 10.1002/j.1460-2075.1989.tb08341.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Esnouf R. M. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model. 1997 Apr;15(2):132-4, 112-3. doi: 10.1016/S1093-3263(97)00021-1. [DOI] [PubMed] [Google Scholar]
  8. Fagan T. F., Ohmiya Y., Blinks J. R., Inouye S., Tsuji F. I. Cloning, expression and sequence analysis of cDNA for the Ca(2+)-binding photoprotein, mitrocomin. FEBS Lett. 1993 Nov 1;333(3):301–305. doi: 10.1016/0014-5793(93)80675-k. [DOI] [PubMed] [Google Scholar]
  9. Fisher A. J., Raushel F. M., Baldwin T. O., Rayment I. Three-dimensional structure of bacterial luciferase from Vibrio harveyi at 2.4 A resolution. Biochemistry. 1995 May 23;34(20):6581–6586. doi: 10.1021/bi00020a002. [DOI] [PubMed] [Google Scholar]
  10. Head J. F., Inouye S., Teranishi K., Shimomura O. The crystal structure of the photoprotein aequorin at 2.3 A resolution. Nature. 2000 May 18;405(6784):372–376. doi: 10.1038/35012659. [DOI] [PubMed] [Google Scholar]
  11. Hendrickson W. A., Horton J. R., LeMaster D. M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 1990 May;9(5):1665–1672. doi: 10.1002/j.1460-2075.1990.tb08287.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hermann A., Cox J. A. Sarcoplasmic calcium-binding protein. Comp Biochem Physiol B Biochem Mol Biol. 1995 Jul;111(3):337–345. doi: 10.1016/0305-0491(94)00218-j. [DOI] [PubMed] [Google Scholar]
  13. Illarionov B. A., Bondar V. S., Illarionova V. A., Vysotski E. S. Sequence of the cDNA encoding the Ca(2+)-activated photoprotein obelin from the hydroid polyp Obelia longissima. Gene. 1995 Feb 14;153(2):273–274. doi: 10.1016/0378-1119(94)00797-v. [DOI] [PubMed] [Google Scholar]
  14. Illarionov B. A., Frank L. A., Illarionova V. A., Bondar V. S., Vysotski E. S., Blinks J. R. Recombinant obelin: cloning and expression of cDNA purification, and characterization as a calcium indicator. Methods Enzymol. 2000;305:223–249. doi: 10.1016/s0076-6879(00)05491-4. [DOI] [PubMed] [Google Scholar]
  15. Inouye S., Noguchi M., Sakaki Y., Takagi Y., Miyata T., Iwanaga S., Miyata T., Tsuji F. I. Cloning and sequence analysis of cDNA for the luminescent protein aequorin. Proc Natl Acad Sci U S A. 1985 May;82(10):3154–3158. doi: 10.1073/pnas.82.10.3154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Inouye S., Tsuji F. I. Cloning and sequence analysis of cDNA for the Ca(2+)-activated photoprotein, clytin. FEBS Lett. 1993 Jan 11;315(3):343–346. doi: 10.1016/0014-5793(93)81191-2. [DOI] [PubMed] [Google Scholar]
  17. Jones T. A., Zou J. Y., Cowan S. W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991 Mar 1;47(Pt 2):110–119. doi: 10.1107/s0108767390010224. [DOI] [PubMed] [Google Scholar]
  18. Kretsinger R. H., Nakayama S. Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins. J Mol Evol. 1993 May;36(5):477–488. doi: 10.1007/BF02406723. [DOI] [PubMed] [Google Scholar]
  19. Kurose K., Inouye S., Sakaki Y., Tsuji F. I. Bioluminescence of the Ca2+-binding photoprotein aequorin after cysteine modification. Proc Natl Acad Sci U S A. 1989 Jan;86(1):80–84. doi: 10.1073/pnas.86.1.80. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Moncrief N. D., Kretsinger R. H., Goodman M. Evolution of EF-hand calcium-modulated proteins. I. Relationships based on amino acid sequences. J Mol Evol. 1990 Jun;30(6):522–562. doi: 10.1007/BF02101108. [DOI] [PubMed] [Google Scholar]
  21. Nicholls A., Sharp K. A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991;11(4):281–296. doi: 10.1002/prot.340110407. [DOI] [PubMed] [Google Scholar]
  22. Nomura M., Inouye S., Ohmiya Y., Tsuji F. I. A C-terminal proline is required for bioluminescence of the Ca(2+)-binding photoprotein, aequorin. FEBS Lett. 1991 Dec 16;295(1-3):63–66. doi: 10.1016/0014-5793(91)81385-l. [DOI] [PubMed] [Google Scholar]
  23. Ohmiya Y., Ohashi M., Tsuji F. I. Two excited states in aequorin bioluminescence induced by tryptophan modification. FEBS Lett. 1992 Apr 20;301(2):197–201. doi: 10.1016/0014-5793(92)81247-j. [DOI] [PubMed] [Google Scholar]
  24. Ohmiya Y., Tsuji F. I. Bioluminescence of the Ca(2+)-binding photoprotein, aequorin, after histidine modification. FEBS Lett. 1993 Apr 12;320(3):267–270. doi: 10.1016/0014-5793(93)80600-y. [DOI] [PubMed] [Google Scholar]
  25. Shimomura O., Johnson F. H. Peroxidized coelenterazine, the active group in the photoprotein aequorin. Proc Natl Acad Sci U S A. 1978 Jun;75(6):2611–2615. doi: 10.1073/pnas.75.6.2611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Strynadka N. C., James M. N. Crystal structures of the helix-loop-helix calcium-binding proteins. Annu Rev Biochem. 1989;58:951–998. doi: 10.1146/annurev.bi.58.070189.004511. [DOI] [PubMed] [Google Scholar]
  27. Terwilliger T. C. Multiwavelength anomalous diffraction phasing of macromolecular structures: analysis of MAD data as single isomorphous replacement with anomalous scattering data using the MADMRG Program. Methods Enzymol. 1997;276:530–537. [PubMed] [Google Scholar]
  28. Tsuji F. I., Ohmiya Y., Fagan T. F., Toh H., Inouye S. Molecular evolution of the Ca(2+)-binding photoproteins of the Hydrozoa. Photochem Photobiol. 1995 Oct;62(4):657–661. doi: 10.1111/j.1751-1097.1995.tb08713.x. [DOI] [PubMed] [Google Scholar]
  29. Vysotski E. S., Liu Z. J., Rose J., Wang B. C., Lee J. Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima. Acta Crystallogr D Biol Crystallogr. 1999 Nov;55(Pt 11):1965–1966. doi: 10.1107/s0907444999011828. [DOI] [PubMed] [Google Scholar]
  30. Wang B. C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 1985;115:90–112. doi: 10.1016/0076-6879(85)15009-3. [DOI] [PubMed] [Google Scholar]
  31. Wnuk W., Schoechlin M., Stein E. A. Regulation of actomyosin ATPase by a single calcium-binding site on troponin C from crayfish. J Biol Chem. 1984 Jul 25;259(14):9017–9023. [PubMed] [Google Scholar]
  32. van Eerd J. P., Takahshi K. Determination of the complete amino acid sequence of bovine cardiac troponin C. Biochemistry. 1976 Mar 9;15(5):1171–1180. doi: 10.1021/bi00650a033. [DOI] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES