One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions

Journal of Molecular Biology

Volumn 321, Issue 5, 2002, Pages 741-765

  Nagano, Nozomi ^a,b   Orengo, Christine A ^a   Thornton, Janet M ^a,c  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Evolution; Functional residues; Phosphate binding motif; TIM barrel

Indexed keywords

PROTEIN; TIM BARREL PROTEIN; TRIOSEPHOSPHATE ISOMERASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; BIODIVERSITY; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CHEMICAL BINDING; ENERGY METABOLISM; HUMAN; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW; SEQUENCE HOMOLOGY;

EID: 0036384350     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00649-6     Document Type: Review

References (44)

1. Farber, G. K. & Petsko, G. A. (1990). The evolution of α/β barrel enzymes. Trends Biochem. Sci. 15, 228-234.
2. Bränden, C. I. (1991). The TIM barrel - the most frequently occurring folding motif in proteins. Curr. Opin. Struct. Biol. 1, 978-983.
3. Wilmanns, M., Hyde, C. C., Davies, D. R., Kirschner, K. & Jansonius, J. N. (1991). Structural conservation in parallel β/α barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry, 30, 9161-9169.
4. Nagano, N., Hutchinson, E. G. & Thornton, J. M. (1999). Barrel structures in proteins - automatic identification and classification including a sequence analysis of TIM barrels. Protein Sci. 8, 2072-2084.
5. Lang, D., Thoma, R., Henn-Sax, M., Sterner, R. & Wilmanns, M. (2000). Structural evidence for evolution of the β/α barrel scaffold by gene duplication and fusion. Science, 289, 1546-1550.
6. Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. (1997). CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
7. Webb, E. C. (1992). Enzyme nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, Academic Press, New York.
8. Branden, C. I. & Tooze, J. (1991). α/β structures. In Introduction to Protein Structure (Bränden, C. I. & Tooze, J., eds), pp. 43-57, Garland Publishing, New York.
9. Reardon, D. & Farber, G. K. (1995). The structure and evolution of α/β barrel proteins. FASEB J. 9, 497-503.
10. 8 barrels: implications for the evolution of metabolic pathways. J. Mol. Biol. 303, 627-640.
11. Fani, R., Lio, P., Chiarelli, I. & Bazzicalupo, M. (1994). The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. J. Mol. Evol. 38, 489-495.
12. 8 glycosidases: sequence and structure analyses suggest distant evolutionary relationships. Protein Eng. 14, 845-855.
13. Bairoch, A. & Apweiler, R. (2000). The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucl. Acids Res. 28, 45-48.
14. Bateman, A., Birney, E., Durbin, R., Eddy, S. R., Finn, R. D. & Sonnhammer, E. L. (1999). Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucl. Acids Res. 27, 260-262.
15. Rouvinen, J., Bergfors, T., Teeri, T., Knowles, J. K. & Jones, T. A. (1990). Three-dimensional structure of cellobiohydrolase II from Trichoderma reesei. Science, 249, 380-386.
16. Spezio, M., Wilson, D. B. & Karplus, P. A. (1993). Crystal structure of the catalytic domain of a thermophilic endocellulase. Biochemistry, 32, 9906-9916.
17. Todd, A. E., Orengo, C. A. & Thornton, J. M. (2001). Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307, 1113-1143.
18. Frishman, D. & Mewes, H. W. (1997). PEDANTic genome analysis. Trends Genet. 13, 415-416.
19. Riley, M. (1998). Genes and proteins of Escherichia coli K-12 (GenProtEC). Nucl. Acids Res. 26, 54.
20. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H. & Kanehisa, M. (1999). KEGG: Kyoto encyclopedia of genes and genomes. Nucl. Acids Res. 27, 29-34.
21. Rison, S. C. G., Hodgman, T. C. & Thornton, J. M. (2000). Comparison of functional annotation schemes for genomes. Funct. Integr. Genom. 1, 56-69.
22. Sharma, V., Grubmeyer, C. & Sacchettini, J. C. (1998). Crystal structure of quinolinic acid phosphoribosyl-transferase from Mmycobacterium tuberculosis: a potential TB drug target. Structure, 6, 1587-1599.
23. Holm, L. & Sander, C. (1997). An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins: Struct. Funct. Genet. 28, 72-82.
24. + channel β subunit. Cell, 97, 943-952.
25. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402.
26. Orengo, C. A. (1999). CORA - topological fingerprints for protein structural families. Protein Sci. 8, 699-715.
27. Schäffer, A. A., Wolf, Y. I., Ponting, C. P., Koonin, E. V., Aravind, L. & Altschul, S. F. (1999). IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 15, 1000-1011.
28. Galperin, M. Y., Aravind, L. & Koonin, E. V. (2000). Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in Archaea. FEMS Microbiol. Letters, 183, 259-264.
29. Taylor, W. R. & Orengo, C. A. (1989). Protein structure alignment. J. Mol. Biol. 208, 1-22.
30. Russell, R. B., Saqi, M. A., Sayle, R. A., Bates, P. A. & Sternberg, M. J. (1997). Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J. Mol. Biol. 269, 423-439.
31. Jia, J., Huang, W., Schorken, U., Sahm, H., Sprenger, G. A., Lindqvist, Y. & Schneider, G. (1996). Crystal structure of transaldolase B from Escherichia coli suggests a circular permutation of the α/β barrel within the class I aldolase family. Structure, 4, 715-724.
32. Kawabata, T. & Nishikawa, K. (2000). Protein tertiary structure comparison using the Markov transition model of evolution. Proteins: Struct. Funct. Genet. 41, 108-122.
33. Sergeev, Y. & Lee, B. (1994). Alignment of β-barrels in (β/α)8 proteins using hydrogen-bonding pattern. J. Mol. Biol. 244, 168-182.
34. Lesk, A. M., Bränden, C. I. & Chothia, C. (1989). Structural principles of a/b barrel proteins: the packing of the interior of the sheet. Proteins: Struct. Funct. Genet. 5, 139-148.
35. Edwards, M. S., Sternberg, M. J. E. & Thornton, J. M. (1987). Structural and sequence patterns in the loops of βαβ units. Protein Eng. 1, 173-181.
36. Scheerlinck, J. P., Lasters, I., Claessens, M., De Maeyer, M., Pio, F., Delhaise, P. & Wodak, S. J. (1992). Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features. Proteins: Struct. Funct. Genet. 12, 299-313.
37. Janecek, S. & Balaz, S. (1995). Functionally essential, invariant glutamate near the C terminus of strand β 5 in various (α/β)8-barrel enzymes as a possible indicator of their evolutionary relatedness. Protein Eng. 8, 809-813.
38. Hall, D. R., Leonard, G. A., Reed, C. D., Watt, C. I., Berry, A. & Hunter, W. N. (1999). The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity. J. Mol. Biol. 287, 383-394.
39. Pearl, F. M. G., Lee, D., Bray, J. E., Sillitoe, I., Todd, A. E., Harrison, A. P. et al. (2000). Assigning genomic sequences to CATH. Nucl. Acids Res. 28, 277-282.
40. Jones, S., Stewart, M., Michie, A., Swindells, M. B., Orengo, C. & Thornton, J. M. (1998). Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci. 7, 233-242.
41. Needleman, S. B. & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
42. Martin, A. C. R., Orengo, C. A., Hutchinson, E. G., Jones, S., Karmirantzou, M., Laskowski, R. A. et al. (1998). Protein folds and functions. Structure, 6, 875-884.
43. Milburn, D., Laskowski, R. A. & Thornton, J. M. (1998). Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. Protein Eng. 11, 855-859.
44. Pearl, F. M. G., Lee, D., Bray, J. E., Buchan, D. W. A., Shepherd, A. J. & Orengo, C. A. (2001). The CATH extended protein-family database providing structural annotations for genome sequences. Protein Sci. 11, 233-244.