Revealing the hidden functional diversity of an enzyme family
Tóm tắt
Từ khóa
Tài liệu tham khảo
Galperin, M.Y. & Koonin, E.V. From complete genome sequence to 'complete' understanding? Trends Biotechnol. 28, 398–406 (2010).
Hanson, A.D., Pribat, A., Waller, J.C. & de Crecy-Lagard, V. 'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list–and how to find it. Biochem. J. 425, 1–11 (2010).
Gifford, L.K., Carter, L.G., Gabanyi, M.J., Berman, H.M. & Adams, P.D. The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. J. Struct. Funct. Genomics 13, 57–62 (2012).
Lukk, T. et al. Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc. Natl. Acad. Sci. USA 109, 4122–4127 (2012).
Furnham, N., Garavelli, J.S., Apweiler, R. & Thornton, J.M. Missing in action: enzyme functional annotations in biological databases. Nat. Chem. Biol. 5, 521–525 (2009).
Huang, H. et al. Divergence of structure and function in the haloacid dehalogenase enzyme superfamily: Bacteroides thetaiotaomicron BT2127 is an inorganic pyrophosphatase. Biochemistry 50, 8937–8949 (2011).
Schnoes, A.M., Brown, S.D., Dodevski, I. & Babbitt, P.C. Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol. 5, e1000605 (2009).
Kreimeyer, A. et al. Identification of the last unknown genes in the fermentation pathway of lysine. J. Biol. Chem. 282, 7191–7197 (2007).
Bellinzoni, M. et al. 3-Keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation. J. Biol. Chem. 286, 27399–27405 (2011).
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109–D114 (2012).
Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 40, D742–D753 (2012).
Deniélou, Y.P., Sagot, M.F., Boyer, F. & Viari, A. Bacterial syntenies: an exact approach with gene quorum. BMC Bioinformatics 12, 193 (2011).
de Melo-Minardi, R.C., Bastard, K. & Artiguenave, F. Identification of subfamily-specific sites based on active sites modeling and clustering. Bioinformatics 26, 3075–3082 (2010).
Strehl, A. & Ghosh, J. Cluster ensembles—a knowledge reuse framework for combining partitionings. J. Mach. Learn. Res. 3, 583–617 (2002).
Pan, H., Bao, W., Xie, Z., Zhang, J. & Li, Y. Molecular cloning and characterization of a cis-epoxysuccinate hydrolase from Bordetella sp. BK-52. J. Microbiol. Biotechnol. 20, 659–665 (2010).
Bao, W. et al. Analysis of essential amino acid residues for catalytic activity of cis-epoxysuccinate hydrolase from Bordetella sp. BK-52. Appl. Microbiol. Biotechnol. http://dx.doi.org/10.1007/s00253-013-5019-2 (2013).
Pelletier, E. et al. “Candidatus Cloacamonas acidaminovorans”: genome sequence reconstruction provides a first glimpse of a new bacterial division. J. Bacteriol. 190, 2572–2579 (2008).
Uanschou, C., Frieht, R. & Pittner, F. What to learn from a comparative genomic sequence analysis of L-carnitine dehydrogenase. Monatsh. Chem. 136, 1365–1381 (2005).
Wargo, M.J. & Hogan, D.A. Identification of genes required for Pseudomonas aeruginosa carnitine catabolism. Microbiology 155, 2411–2419 (2009).
Bar-Even, A. et al. The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 50, 4402–4410 (2011).
Collier, L.S., Gaines, G.L. III & Neidle, E.L. Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator. J. Bacteriol. 180, 2493–2501 (1998).
Yalpani, M., Willecke, K. & Lynen, F. Triacetic acid lactone, a derailment product of fatty acid biosynthesis. Eur. J. Biochem. 8, 495–502 (1969).
Xie, D. et al. Microbial synthesis of triacetic acid lactone. Biotechnol. Bioeng. 93, 727–736 (2006).
Monticello, D.J. & Costilow, R.N. Interconversion of valine and leucine by Clostridium sporogenes. J. Bacteriol. 152, 946–949 (1982).
Magrane, M. & Consortium, U. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011, bar009 (2011).
Howe, K., Bateman, A. & Durbin, R. QuickTree: building huge neighbour-joining trees of protein sequences. Bioinformatics 18, 1546–1547 (2002).
Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005).
Brown, D.P., Krishnamurthy, N. & Sjolander, K. Automated protein subfamily identification and classification. PLoS Comput. Biol. 3, e160 (2007).
Fisher, D. Knowledge acquisition via incremental conceptual clustering. Mach. Learn. 2, 139–172 (1987).
Puranen, J.S., Vainio, M.J. & Johnson, M.S. Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. J. Comput. Chem. 31, 1722–1732 (2010).
Pettersen, E.F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Trott, O. & Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455–461 (2010).
Rozen, S. & Skaletsky, H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132, 365–386 (2000).
Ralser, M. et al. An efficient and economic enhancer mix for PCR. Biochem. Biophys. Res. Commun. 347, 747–751 (2006).
Aslanidis, C. & de Jong, P.J. Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 18, 6069–6074 (1990).
Moriyama, T. & Srere, P.A. Purification of rat heart and rat liver citrate synthases. Physical, kinetic, and immunological studies. J. Biol. Chem. 246, 3217–3223 (1971).
Swart, M., Snijders, J.G. & van Duijnenb, Th.P. Polarizabilities of amino acid residues. J. Comp. Meth. Sci. Eng. 4, 419–425 (2004).