Abstract
The use of selenomethionine as a phasing tool was first reported in 1990. Engineering of selenomethionyl proteins for structure determination is now routine. In fact, selenium is by far the most commonly used anomalous scatterer for multiwavelength anomalous diffraction studies. The past few years have seen new developments, which demonstrated the feasibility of expressing selenomethionyl protein in eukaryotic systems. In this chapter, the different methods available for producing selenomethionine-labeled proteins in bacteria, as well as in yeast and mammalian cells will be presented, along with tips for purifying and crystallizing selenomethionyl proteins.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hendrickson, W. A., Horton, J. R. and LeMaster, D. M. (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665ā1672.
Bernard, A. R., Wells, T. N., Cleasby, A., Borlat, F., Payton, M. A., and Proudfoot, A. E. (1995). Selenomethionine labelling of phosphomannose isomerase changes its kinetic properties. Eur. J. Biochem. 230, 111ā118.
Gassner, N. C., Baase, W. A., Hausrath, A. C., and Matthews, B. W. (1999) Substitution with selenomethionine can enhance the stability of methionine-rich proteins. J. Mol. Biol. 294, 17ā20.
Jiang, J. and Sweet, R. M. (2004) Protein Data Bank depositions from synchrotron sources. J. Synchrotron. Radiat. 11, 319ā327.
Sambrook, J. and Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
Sreenath, H. K., Bingman, C. A., Buchan, B. W., et al. (2005) Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium. Protein Expr. Purif. 40, 256ā267.
Cowie, D. B. and Cohen, G. N. (1957) Biosynthesis by E. coli of active altered proteins containing selenium instead of sulfur. Biochim. Biophys. Acta 26, 252ā261.
DoubliĆ©, S. (1997) Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276, 523ā530.
Berne, P. F., DoubliƩ, S., and Carter, C. W., Jr. (1999) Molecular biology for structural biology. In: Crystallization of Nucleic Acids and Proteins, 2nd ed., (Ducruix, A. and GiegƩ, R., eds.), Oxford University Press, Oxford, UK.
Van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L. and Clardy, J. (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and Rapamycin. J. Mol. Biol. 229, 105ā124.
Studier, F. W. (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207ā234.
Bushnell, D. A., Cramer, P., and Kornberg, R. D. (2001) Selenomethionine incorporation in Saccharomyces cerevisiae RNA polymerase II. Structure (Camb) 9, R11āR14.
Larsson, A. M., Stahlberg, J., and Jones, T. A. (2002) Preparation and crystallization of selenomethionyl dextranase from Penicillium minioluteum expressed in Pichia pastoris. Acta Crystallogr. D Biol. Crystallogr. 58, 346ā348.
Xu, B., Munoz, I. I., Janson, J. C., and Stahlberg, J. (2002) Crystallization and X-ray analysis of native and selenomethionyl beta-mannanase Man5A from blue mussel, Mytilus edulis, expressed in Pichia pastoris. Acta Crystallogr. D Biol. Crystallogr. 58, 542ā545.
Larsson, A. M., Andersson, R., Stahlberg, J., Kenne, L., and Jones, T. A. (2003) Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex. Structure (Camb) 11, 1111ā1121.
Cramer, P., Bushnell, D. A., Fu, J., et al. (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288, 640ā649.
McWhirter, S. M., Pullen, S. S., Holton, J. M., Crute, J. J., Kehry, M. R., and Alber, T. (1999). Crystallographic analysis of CD40 recognition and signaling by human TRAF2. Proc. Natl. Acad. Sci. USA 96, 8408ā8413.
Aertgeerts, K., Ye, S., Tennant, M. G., et al. (2004) Crystal structure of human dipeptidyl peptidase IV in complex with a decapeptide reveals details on substrate specificity and tetrahedral intermediate formation. Protein Sci, 13, 412ā421.
Bellizzi, J. J., Widom, J., Kemp, C. W., and Clardy, J. (1999) Producing selenomethionine-labeled proteins with a baculovirus expression vector system. Structure Fold. Des. 7, R263āR267.
Ogiso, H., Ishitani, R., Nureki, O., et al. (2002) Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell 110, 775ā787.
Hamaoka, B. Y., Dann, C. E., 3rd, Geisbrecht, B. V., and Leahy, D. J. (2004) Crystal structure of Caenorhabditis elegans HER-1 and characterization of the interaction between HER-1 and TRA-2A. Proc. Natl. Acad. Sci. USA 101, 11,673ā11,678.
Davis, S. J., Ikemizu, S., Collins, A. V., et al. (2001) Crystallization and functional analysis of a soluble deglycosylated form of the human costimulatory molecule B7-1. Acta Crystallogr. D Biol. Crystallogr. 57, 605ā608.
Carfi, A., Smith, C. A., Smolak, P. J., McGrew, J., and Wiley, D. C. (1999) Structure of a soluble secreted chemokine inhibitor vCCI (p35) from cowpox virus. Proc. Natl. Acad. Sci. USA 96, 12,379ā12,383.
Wu, H., Lustbader, J. W., Liu, Y., Canfield, R. E., and Hendrickson, W. A. (1994) Structure of human chorionic gonadotropin at 2.6 A resolution from MAD analysis of the selenomethionyl protein. Structure 2, 545ā558.
Lustbader, J. W., Wu, H., Birken, S., et al. (1995) The expression, characterization, and crystallization of wild-type and selenomethionyl human chorionic gonadotropin. Endocrinology 136, 640ā650.
May, A. P., Robinson, R. C., Aplin, R. T., Bradfield, P., Crocker, P. R., and Jones, E. Y. (1997) Expression, crystallization, and preliminary X-ray analysis of a sialic acid-binding fragment of sialoadhesin in the presence and absence of ligand. Protein Sci. 6, 717ā721.
Wally, J., Halbrook, P. J., Vonrhein, C., et al. (2006) The crystal structure of iron-free human serum transferring provides insight into inter-lobe communication and receptor binding. J. Biol. Chem., in press.
Kigawa, T., Yamaguchi-Nunokawa, E., Kodama, K., et al. (2002) Selenomethionine incorporation into a protein by cell-free synthesis. J. Struct. Funct. Genomics 2, 29ā35.
Yokoyama, S. (2003) Protein expression systems for structural genomics and proteomics. Curr. Opin. Chem. Biol. 7, 39ā43.
Hendrickson, W. A. and Ogata, C. M. (1997) Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol. 276, 494ā523.
Strub, M. P., Hoh, F., Sanchez, J. F., et al. (2003) Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing. Structure (Camb) 11, 1359ā1367.
Smith, J. L. and Thompson, A. (1998) Reactivity of selenomethionine: dents in the magic bullet? Structure 6, 815ā819.
Sharff, A. J., Koronakis, E., Luisi, B., and Koronakis, V. (2000) Oxidation of selenomethionine: some MADness in the method! Acta Crystallogr. D Biol. Crystallogr. 56, 785ā788.
Thomazeau, K., Curien, G., Thompson, A., Dumas, R., and Biou, V. (2001) MAD on threonine synthase: the phasing power of oxidized selenomethionine. Acta Crystallogr. D Biol. Crystallogr. 57, 1337ā1340.
Boggon, T. J. and Shapiro, L. (2000) Screening for phasing atoms in protein crystallography. Structure Fold. Des. 8, R143āR149.
Leahy, D. J., Erickson, H. P., Aukhil, I., Joshi, P., and Hendrickson, W. A. (1994) Crystallization of a fragment of human fibronectin: introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine. Proteins 19, 48ā54.
Skinner, M. M., Zhang, H., Leschnitzer, D. H., et al. (1994) Structure of the gene V protein of bacteriophage f1 determined by multiwavelength X-ray diffraction on the selenomethionyl protein. Proc. Natl. Acad. Sci. USA 91, 2071ā2075.
Jones, D. T., Taylor, W. R., and Thornton, J. M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275ā282.
Cohen, S. L. and Chait, B. T. (2001) Mass spectrometry as a tool for protein crystallography. Annu. Rev. Biophys. Biomol. Struct. 30, 67ā85.
Hagemeier, C. H., Shima, S., Warkentin, E., Thauer, R. K., and Ermler, U. (2003) Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase from Methanopyrus kandleri: the selenomethionine-labelled and non-labelled enzyme crystallized in two different forms. Acta Crystallogr. D Biol. Crystallogr. 59, 1653ā1655.
McAuley, K. E., Cummins, I., Papiz, M., Edwards, R., and Fordham-Skelton, A. P. (2003). Purification, crystallization and preliminary X-ray diffraction analysis of S-formylglutathione hydrolase from Arabidopsis thaliana: effects of pressure and selenomethionine substitution on space-group changes. Acta Crystallogr. D Biol. Crystallogr. 59, 2272ā2274.
Poulsen, J. C., Harris, P., Jensen, K. F., and Larsen, S. (2001) Selenomethionine substitution of orotidine-5ā²-monophosphate decarboxylase causes a change in crystal contacts and space group. Acta Crystallogr. D Biol. Crystallogr. 57, 1251ā1259.
Witkowski, A. and Smith, S. (1998) Successful expression of a selenomethionyl protein under control of the temperature-sensitive lambda repressor requires higher than normal temperature. Biotechniques 24, 934ā936.
Dong, C., Kotzsch, A., Dorward, M., van Pee, K. H., and Naismith, J. H. (2004) Crystallization and X-ray diffraction of a halogenating enzyme, tryptophan 7-halogenase, from Pseudomonas fluorescens. Acta Crystallogr. D Biol. Crystallogr. 60, 1438ā1440.
Millard, C. S., Stols, L., Quartey, P., Kim, Y., Dementieva, I., and Donnelly, M. I. (2003) A less laborious approach to the high-throughput production of recombinant proteins in Escherichia coli using 2-liter plastic bottles. Protein Expr. Purif. 29, 311ā320.
Stols, L., Millard, C. S., Dementieva, I., and Donnelly, M. I. (2004) Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination. J. Struct. Funct. Genomics 5, 95ā102.
OāReilly, D. R. and Miller, L. K. (1988) Expression and complex formation of simian virus 40 large T antigen and mouse p53 in insect cells. J. Virol. 62, 3109ā3119.
Stein, A. J., Fuchs, G., Fu, C., Wolin, S. L., and Reinisch, K. M. (2005) Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity. Cell 121, 529ā539.
Gassner, N. C. and Matthews, B. W. (1999) Use of differentially substituted selenomethionine proteins in X-ray structure determination. Acta Crystallogr. D Biol. Crystallogr. 55, 1967ā1970.
Bateman, K. S., Brownie, E. R., Wolodko, W. T., and Fraser, M. E. (2002) Structure of the mammalian CoA transferase from pig heart. Biochemistry 41, 14,455ā14,462.
Carfi, A., Gong, H., Lou, H., et al. (2002) Crystallization and preliminary diffraction studies of the ectodomain of the envelope glycoprotein D from herpes simplex virus 1 alone and in complex with the ectodomain of the human receptor HveA. Acta Crystallogr. D Biol. Crystallogr. 58, 836ā838.
Chen, W. Y. and Bahl, O. P. (1991) Selenomethionyl analog of recombinant human choriogonadotropin. J. Biol. Chem. 266, 9355ā9358.
Liemann, S., Chandran, K., Baker, T. S., Nibert, M. L., and Harrison, S. C. (2002) Structure of the reovirus membrane-penetration protein, Mu1, in a complex with is protector protein, Sigma3. Cell 108, 283ā295.
Fremont, D. H., Crawford, F., Marrack, P., Hendrickson, W. A., and Kappler, J. (1998) Crystal structure of mouse H2-M. Immunity 9, 385ā393.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
Ā© 2007 Humana Press Inc.
About this protocol
Cite this protocol
DoubliƩ, S. (2007). Production of Selenomethionyl Proteins in Prokaryotic and Eukaryotic Expression Systems. In: Walker, J.M., DoubliƩ, S. (eds) Macromolecular Crystallography Protocols. Methods in Molecular Biology, vol 363. Humana Press. https://doi.org/10.1007/978-1-59745-209-0_5
Download citation
DOI: https://doi.org/10.1007/978-1-59745-209-0_5
Publisher Name: Humana Press
Print ISBN: 978-1-58829-292-6
Online ISBN: 978-1-59745-209-0
eBook Packages: Springer Protocols