Cradle-loop barrels and the concept of metafolds in protein classification by natural descent

Current Opinion in Structural Biology

Volumn 18, Issue 3, 2008, Pages 358-365

  Alva, Vikram ^a   Koretke, Kristin K ^b   Coles, Murray ^a   Lupas, Andrei N ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^b GLAXOSMITHKLINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BIOINFORMATICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; PYROCOCCUS HORIKOSHII; REVIEW; SEQUENCE ANALYSIS;

MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 44949143819     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2008.02.006     Document Type: Review

References (26)

1. Dietmann S., Park J., Notredame C., Heger A., Lappe M., and Holm L. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res 29 (2001) 55-57
2. Greene L.H., Lewis T.E., Addou S., Cuff A., Dallman T., Dibley M., Redfern O., Pearl F., Nambudiry R., Reid A., et al. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 35 (2007) D291-D297
3. Andreeva A., Howorth D., Chandonia J.M., Brenner S.E., Hubbard T.J., Chothia C., and Murzin A.G. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36 (2008) D419-D425
4. Hadley C., and Jones D.T. A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure 7 (1999) 1099-1112
5. Day R., Beck D.A., Armen R.S., and Daggett V. A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. Protein Sci 12 (2003) 2150-2160
6. Grishin N.V. Fold change in evolution of protein structures. J Struct Biol 134 (2001) 167-185
7. Kinch L.N., and Grishin N.V. Evolution of protein structures and functions. Curr Opin Struct Biol 12 (2002) 400-408
8. •] describe examples of homologous fold change by a range of different mechanisms. The level of structural insight displayed in both papers is impressive.
9. •], this article presents examples of homologous fold change. In addition, it introduces a database of manually curated structural alignments, which allows users to explore the fold changes interactively.
10. Lupas A.N., and Koretke K.K. Evolution of protein folds. In: Peitsch M., and Schwede T. (Eds). Computational Structural Biology (2008), World Scientific Publishing Co.
11. Coles M., Diercks T., Liermann J., Groger A., Rockel B., Baumeister W., Koretke K.K., Lupas A., Peters J., and Kessler H. The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. Curr Biol 9 (1999) 1158-1168
12. Castillo R.M., Mizuguchi K., Dhanaraj V., Albert A., Blundell T.L., and Murzin A.G. A six-stranded double-psi beta barrel is shared by several protein superfamilies. Structure 7 (1999) 227-236
13. Coles M., Hulko M., Djuranovic S., Truffault V., Koretke K., Martin J., and Lupas A.N. Common evolutionary origin of swapped-hairpin and double-psi beta barrels. Structure 14 (2006) 1489-1498. This paper establishes the homologous relationship between DNA-binding swapped-hairpin barrels and double-psi barrels with chaperone activity via proteins with an intermediate topology, which are most likely also DNA binding.
14. Coles M., Djuranovic S., Soding J., Frickey T., Koretke K., Truffault V., Martin J., and Lupas A.N. AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels. Structure 13 (2005) 919-928
15. Ammelburg M., Hartmann M.D., Djuranovic S., Alva V., Koretke K.K., Martin J., Sauer G., Truffault V., Zeth K., Lupas A.N., et al. A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Structure 15 (2007) 1577-1590. This paper makes two important contributions. It provides the first characterization of an archaeal riboflavin kinase and it shows that archaeal riboflavin kinases are intermediate in sequence between basal, DNA-binding cradle-loop barrels and bacterial and eukaryotic riboflavin kinases, providing an evolutionary bridge. The paper makes predictions about the sequence of mutations necessary to transform a DNA-binding protein into an enzyme, first bringing about CTP binding and subsequently conferring the ability to transfer the γ-phosphate to riboflavin.
16. Hulko M., Lupas A.N., and Martin J. Inherent chaperone-like activity of aspartic proteases reveals a distant evolutionary relation to double-psi barrel domains of AAA-ATPases. Protein Sci 16 (2007) 644-653
17. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (2005) 951-960
18. The GenBank entry in Wikipedia. http://en.wikipedia.org/wiki/GenBank.
19. The Genomes OnLine Database v 2.0. http://www.genomesonline.org/gold_statistics.htm.
20. The PDB Statistics hyperlink on the Protein Data Bank home page. http://www.rcsb.org/pdb/statistics/contentGrowthChart.do?content=total&seqid=100.
21. The InterPro database. http://www.ebi.ac.uk/interpro/.
22. Marsden R.L., Lewis T.A., and Orengo C.A. Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinformatics 8 (2007) 86. Structural genomics approaches are essential for a comprehensive structural characterization of proteins. This paper presents an excellent description of the current structural coverage of protein families and discusses further developments needed to bring this effort to a successful conclusion.
23. Burley S.K., and Bonanno J.B. Structuring the universe of proteins. Annu Rev Genomics Hum Genet 3 (2002) 243-262
24. Taylor W.R. Evolutionary transitions in protein fold space. Curr Opin Struct Biol 17 (2007) 354-361
25. Kolodny R., Petrey D., and Honig B. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol 16 (2006) 393-398
26. Honig B. Protein structure space is much more than the sum of its folds. Nat Struct Mol Biol 14 (2007) 458