Acknowledgement
Supported by : Korea Research Foundation, Ministry of Health & Welfare
References
- Bendtsen, J. D., Nielsen, H., von Heijne, G., and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783-795 https://doi.org/10.1016/j.jmb.2004.05.028
- Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921 https://doi.org/10.1107/S0907444998003254
- D'Andrea, L. D. and Regan, L. (2003) TPR proteins: the versatile helix. Trends Biochem. Sci. 28, 655-662 https://doi.org/10.1016/j.tibs.2003.10.007
- Das, A. K., Cohen, P. W., and Barford, D. (1998) The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions. EMBO J. 17, 1192-1199 https://doi.org/10.1093/emboj/17.5.1192
- DeLano, W. L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, (http://www.pymol. org)
- Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132 https://doi.org/10.1107/S0907444904019158
- Gatto, G. J. J., Geisbrecht, B. V., Gould, S. J., and Berg, J. M. (2000) Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Nat. Struct. Biol. 7, 1091-1095 https://doi.org/10.1038/81930
- Georis, J., de Lemos Esteves, F., Lamotte-Brasseur, J., Bougnet, V., Devreese, B., et al. (2000) An additional aromatic interaction improves the thermostability and thermophilicity of a mesophilic family 11 xylanase: structural basis and molecular study. Protein Sci. 9, 466-475 https://doi.org/10.1110/ps.9.3.466
- Harp, J. M., Timm, D. E., and Bunick, G. J. (1998) Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography. Acta Crystallogr. D Biol. Crystallogr. 54, 622-628 https://doi.org/10.1107/S0907444997019008
- Henne, A., Bruggemann, H., Raasch, C., Wiezer, A., Hartsch, T., et al. (2004) The genome sequence of the extreme thermophile Thermus thermophilus. Nat. Biotechnol. 22, 547-553 https://doi.org/10.1038/nbt956
- Ikai, A. (1980) Thermostability and aliphatic index of globular proteins; in J Biochem (Tokyo) Vol. 88, pp. 1895-1898
- Jinek, M., Rehwinkel, J., Lazarus, B. D., Izaurralde, E., Hanover, J. A., et al. (2004) The superhelical TPR-repeat domain of Olinked GlcNAc transferase exhibits structural similarities to importin alpha. Nat. Struct. Mol. Biol. 11, 1001-1007 https://doi.org/10.1038/nsmb833
- Kim, K., Oh, J., Han, D., Kim, E. E., Lee, B., et al. (2006) Crystal structure of PilF: functional implication in the type 4 pilus biogenesis in Pseudomonas aeruginosa. Biochem. Biophys. Res. Commun. 340, 1028-1038 https://doi.org/10.1016/j.bbrc.2005.12.108
- Krissinel, E. and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D Biol. Crystallogr. 60, 2256-2268 https://doi.org/10.1107/S0907444904026460
- Kumar, S., Tsai, C. J., and Nussinov, R. (2000) Factors enhancing protein thermostability. Proteine Eng. 13, 179-191 https://doi.org/10.1093/protein/13.3.179
- Kyte, J. and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132 https://doi.org/10.1016/0022-2836(82)90515-0
- Kyte J, D. R. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132 https://doi.org/10.1016/0022-2836(82)90515-0
- Lapouge, K., Smith, S. J., Walker, P. A., Gamblin, S. J., Smerdon, S. J., et al. (2000) Structure of the TPR domain of p67phox in complex with Rac.GTP. Mol. Cell 6, 899-907 https://doi.org/10.1016/S1097-2765(05)00091-2
- Lasa, I. and Berenguer, J. (1993) Thermophilic enzymes and their biotechnological potential. Microbiologia 9, 77-89
- Lee, D., Won, J. H., Auh, C. K., and Park, Y. M. (2003) Purification and characterization of a cytosolic phospholipase A2 from rat liver. Mol. Cells 16, 361-367
- Letunic, I., Copley, R. R., Pils, B., Pinkert, S., Schultz, J., et al. (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 34, D257-260 https://doi.org/10.1093/nar/gkj079
- Luan, C. H., Qiu, S., Finley, J. B., Carson, M., Gray, R. J., et al. (2004) High-throughput expression of C. elegans proteins. Genome Res. 14, 2102-2110 https://doi.org/10.1101/gr.2520504
- Magliery, T. J. and Regan, L. (2004) Beyond consensus: statistical free energies reveal hidden interactions in the design of a TPR motif. J. Mol. Biol. 343, 731-745 https://doi.org/10.1016/j.jmb.2004.08.026
- Matthews, B. W. (1968) Solvent content of protein crystals. J. Mol. Biol. 33, 491-497 https://doi.org/10.1016/0022-2836(68)90205-2
- Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1-6 https://doi.org/10.1093/protein/10.1.1
- Novotny, M., Madsen, D., and Kleywegt, G. J. (2004) Evaluation of protein fold comparison servers. Proteins 54, 260-270 https://doi.org/10.1002/prot.10553
- Otwinowski, Z. and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods Enzymol. 276, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X
- Pallen, M. J., Francis, M. S., and Futterer, K. (2003) Tetratricopeptide- like repeats in type-III-secretion chaperones and regulators. FEMS Microbiol. Lett. 223, 53-60 https://doi.org/10.1016/S0378-1097(03)00344-6
- Passmore, L. A., Booth, C. R., Venien-Bryan, C., Ludtke, S. J., Fioretto, C., et al. (2005) Structural analysis of the anaphasepromoting complex reveals multiple active sites and insights into polyubiquitylation. Mol. Cell 20, 855-866 https://doi.org/10.1016/j.molcel.2005.11.003
- Perrakis, A., Morris, R., and Lamzin, V. S. (1999) Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458-463 https://doi.org/10.1038/8263
- Perry, A. J., Hulett, J. M., Likic, V. A., Lithgow, T., and Gooley, P. R. (2006) Convergent evolution of receptors for protein import into mitochondria. Curr. Biol. 16, 221-229 https://doi.org/10.1016/j.cub.2005.12.034
- Rittinger, K., Budman, J., Xu, J., Volinia, S., Cantley, L. C., et al. (1999) Structural analysis of 14-3-3 phosphopeptide complexes identifies a dual role for the nuclear export signal of 14- 3-3 in ligand binding. Mol. Cell 4, 153-166 https://doi.org/10.1016/S1097-2765(00)80363-9
- Schultz, J., Milpetz, F., Bork, P., and Ponting, C. P. (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl. Acad. Sci. USA 95, 5857-5864
- Sikorski, R. S., Boguski, M. S., Goebl, M., and Hieter, P. (1990) A repeating amino acid motif in CDC23 defines a family of proteins and a new relationship among genes required for mitosis and RNA synthesis. Cell 60, 307-317 https://doi.org/10.1016/0092-8674(90)90745-Z
- Steegborn, C., Danot, O., Huber, R., and Clausen, T. (2001) Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization. Structure 9, 1051-1060 https://doi.org/10.1016/S0969-2126(01)00665-7
- Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997) A genomic perspective on protein families. Science 278, 631-637 https://doi.org/10.1126/science.278.5338.631
- Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22-28 https://doi.org/10.1093/nar/29.1.22
- Terwilliger, T. C. and Berendzen, J. (1999) Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55, 849-861 https://doi.org/10.1107/S0907444999000839
- Terwilliger, T. C. and Berendzen, J. (2000) Maximum-likelihood density modification. Acta Crystallogr. D Biol Crystallogr. 56, 965-972 https://doi.org/10.1107/S0907444900005072
- Terwilliger, T. C. and Berendzen, J. (2003) Automated mainchain model building by template matching and iterative fragment extension. Acta Crystallogr. D Biol. Crystallogr. 59, 38-44 https://doi.org/10.1107/S0907444902018036
- Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 https://doi.org/10.1093/nar/22.22.4673
- von Mering, C., Huynen, M. A., Jaeggi, D., Schmidt, S., Bork, P., et al. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31, 258-261 https://doi.org/10.1093/nar/gkg034
- von Mering, C., Jensen, L. J., Snel, B., Hooper, S. D., Krupp, M., et al. (2005) STRING: known and predicted proteinprotein associations, integrated and transferred across organisms. Nucleic Acids Res. 33, D433-437 https://doi.org/10.1093/nar/gki005
- Wilkins, M. R., Gasteiger, E., Bairoch, A., Sanchez, J. C., Williams, K. L., et al. (1999) Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. 112, 531-552
- Wilson, C. G., Kajander, T., and Regan, L. (2005) The crystal structure of NlpI. A prokaryotic tetratricopeptide repeat protein with a globular fold. FEBS J. 272, 166-179 https://doi.org/10.1111/j.1432-1033.2004.04397.x
- Winn, M. D., Ashton, A. W., Briggs, P. J., Ballard, C. C., and Patel, P. (2002) Ongoing developments in CCP4 for highthroughput structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1929-1936 https://doi.org/10.1107/S0907444902016116
- Zhang, M., Windheim, M., Roe, S., Peggie, M., Cohen, P., et al. (2005) Chaperoned ubiquitylation--crystal structures of the CHIP U box E3 ubiquitin ligase and a CHIP-Ubc13-Uev1a complex. Mol. Cell 20, 525-538 https://doi.org/10.1016/j.molcel.2005.09.023