Using the Structure‐Function Linkage Database to Characterize Functional Domains in Enzymes
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Abstract
The Structure?Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web?accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of newly sequenced enzymes and to correct misannotated functional assignments for enzymes currently in public databases. It is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases.
Keywords: superfamily analysis; sequence analysis; structure?function relationships; function prediction; annotation transfer
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- Basic Protocol 1: Using the SFLD to Predict the Function of an Uncharacterized Enzyme
- Basic Protocol 2: Using the SFLD to Correct Misannotated Functional Assignments
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
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Figure 2.10.1 The SFLD homepage. View Image -
Figure 2.10.2 The SFLD Search by Enzyme page with a protein sequence pasted into the Protein Sequence box. View Image -
Figure 2.10.3 SFLD sequence search results. Results are displayed in tabular format, sorted by HMMER E‐value. View Image -
Figure 2.10.4 Alignment of a query sequence with the SFLD galactonate dehydratase family. The query sequence is the top sequence in the alignment. View Image -
Figure 2.10.5 Alignment of a query sequence with the SFLD galactonate dehydratase family. Family‐specific catalytic residues are automatically highlighted. Note that the catalytic residue position numbering given in the table below the alignment is keyed to an alignment without a query sequence, and therefore may not correspond to the numbering on alignments that include query sequences. View Image -
Figure 2.10.6 A dendrogram of the SFLD galactonate dehydratase family, plus a query sequence. View Image -
Figure 2.10.7 The SFLD family page for the galactonate dehydratase family. View Image -
Figure 2.10.8 The SFLD family page for the muconate cycloisomerase family. Note the second display panel, which provides a pictorial view of the active site for a representative family member with a solved crystal structure. View Image -
Figure 2.10.9 The NCBI homepage with Protein selected in the Search listbox and gi number 23100420 specified as the protein sequence for which to search. View Image -
Figure 2.10.10 NCBI summary protein search results for gi number 23100420. View Image -
Figure 2.10.11 The SFLD Browse by Reaction page. View Image -
Figure 2.10.12 Alignment of a query sequence with the SFLD muconate cycloisomerase family. Family‐specific catalytic residues are automatically highlighted. View Image
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Literature Cited
| Babbitt, P.C. and Gerlt, J.A. 1997. Understanding enzyme superfamilies: Chemistry as the fundamental determinant in the evolution of new catalytic activities. J. Biol. Chem. 272:30591‐30594. | |
| Babbitt, P.C., Mrachko, G.T., Hasson, M.S., Huisman, G.W., Kolter, R., Ringe, D., Petsko, G.A., Kenyon, G.L., and Gerlt, J.A. 1995. A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids. Science 267:1159‐1161. | |
| Brenner, S.E. 1999. Errors in genome annotation. Trends Genet. 15:132‐133. | |
| Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G., and Thompson, J.D. 2003. Multiple sequence alignment with the Clustal series of programs. Nucl. Acids Res. 31:3497‐3500. | |
| Deacon, J. and Cooper, R.A. 1977. D‐Galactonate utilisation by enteric bacteria: The catabolic pathway in Escherichia coli. FEBS Lett. 77:201‐205. | |
| Devos, D. and Valencia, A. 2001. Intrinsic errors in genome annotation. Trends Genet. 17:429‐431. | |
| Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14:755‐763. | |
| Eulberg, D., Lakner, S., Golovleva, L.A., and Schlomann, M. 1998. Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus 1CP: Evidence for a merged enzyme with 4‐carboxymuconolactone‐decarboxylating and 3‐oxoadipate enol‐lactone‐hydrolyzing activity. J. Bacteriol. 180:1072‐1081. | |
| Gerlt, J.A. and Babbitt, P.C. 2001. Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem. 70:209‐246. | |
| Gilks, W.R., Audit, B., De Angelis, D., Tsoka, S., and Ouzounis, C.A. 2002. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 18:1641‐1649. | |
| Horowitz, N.H. 1945. On the evolution of biochemical syntheses. Proc. Natl. Acad. Sci. U.S.A. 31:153‐157. | |
| Horowitz, N.H. 1965. The evolution of biochemical syntheses: Retrospect and prospect. In Evolving Genes and Proteins (V. Bryson and H.J. Vogel, eds.) pp. 15‐23. Academic Press, New York. | |
| Jensen, R.A. 1976. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30:409‐425. | |
| Pegg, S.C., Brown, S., Ojha, S., Huang, C.C., Ferrin, T.E., and Babbitt, P.C. 2005. Representing structure‐function relationships in mechanistically diverse enzyme superfamilies. Pac. Symp. Biocomput. 2005:358‐369. | |
| Petsko, G.A., Kenyon, G.L., Gerlt, J.A., Ringe, D., and Kozarich, J.W. 1993. On the origin of enzymatic species. Trends Biochem. Sci. 18:372‐376. | |
| Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. 2004. UCSF Chimera: A visualization system for exploratory research and analysis. J. Comput. Chem. 25:1605‐1612. | |
| Rison, S.C., Teichmann, S.A., and Thornton, J.M. 2002. Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J. Mol. Biol. 318:911‐932. | |
| Teichmann, S.A., Rison, S.C., Thornton, J.M., Riley, M., Gough, J., and Chothia, C. 2001. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J. Mol. Biol. 311:693‐708. | |
| Todd, A.E., Orengo, C.A., and Thornton, J.M. 2001. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:1113‐1143. | |
| Weininger, D. 1988. SMILES, a chemical language and information system. 1: Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28:31‐36. | |
| Key References | |
| Pegg et al., 2005. See above. | |
| Describes the SFLD. | |
| Gerlt and Babbitt, 2001. See above. | |
| Describes various mechanisms of enzyme evolution, including chemistry‐driven evolution of mechanistically diverse superfamilies. Several mechanistically diverse superfamilies are discussed in detail. | |
| Babbitt et al., 1995. See above. | |
| Describes the use of superfamily analysis to elucidate the function of an uncharacterized ORF in Escherichia coli. | |
| Internet Resources | |
| http://sfld.rbvi.ucsf.edu/ | |
| The Structure‐Function Linkage Database. | |
| http://theseed.uchicago.edu/FIG/index.cgi | |
| Get operon context information for a specific gene. | |
| http://modbase.compbio.ucsf.edu/modbase‐cgi‐new/search_form.cgi | |
| View modeled 3‐D structures for a specific protein. |
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