There has been no enzyme classification that has considered 3D-structures and catalytic mechanisms. Therefore, I will create a novel enzyme classification database, by analyzing and classifying enzyme functions, that is, catalytic mechanisms, based on the reaction types, each reaction step and structures of enzyme, cofactor, and substrate/product. Based on the all the information, I am now developing a new enzyme classification, which can substitute for the conventional classification, Enzyme Commission Number. Moreover, considering the stereochemistry, I will visualize the catalytic mechanisms, in order to develop novel functions.
EzCatDB: A database of Enzyme Catalytic Mechanisms
PRESTO: Funded by Japan Science and Technology Corporation (JST) (December 2001-November 2004)
(1) Nagano, Nozomi., Saito, Kazuki., Toriyama, Masaru., Imoto, Masakatsu. and Nakajima, Terumi. Mastoparan analog to elevate fertilization membrane of sea urchin eggs. In: "Peptide Chemistry 1992." Proceedings of the 2nd Japan Symposium on Peptide Chemistry. (eds. Yanaihara, N.) ESCOM (1992) 356-358
(2) Saito, K., Imoto, M., Nagano, N., Toriyama, M. and Nakajima, T. Such hydrophobic peptides as dansylated mastoparan can elevate the fertilization membrane of sea urchin eggs. (1995) Biochem. Biophys. Res. Commun. 215, 828-834.
(3) Nagano, Kozo. & Nagano, Nozomi. Transfer RNA docking pair model in the ribosomal pre- and post-translocational states. (1997) Nucleic Acids Res., 25, 1254-1264.
(4) Kozo Nagano & Nozomi Nagano (1997) Mechanism of decoding mRNA in Protein Biosynthesis (YAKUGAKU ZASSHI) 117, 749-763.
(5) David Gilbert, David Westhead, Nozomi Nagano & Janet Thornton (1999) Motif-based searching in TOPS protein topology databases. Bioinformatics, 15, 317-326.
(6) Nozomi Nagano, Motonori Ota & Ken Nishikawa (1999) Strong hydrophobic nature of cysteine residues in proteins. FEBS Lett. 458, 69-71.
(7) Nozomi Nagano, Gail Hutchinson & Janet Thornton (1999) Barrel structures in proteins - Automatic identification and classification including a sequence analysis of TIM barrels. Protein Sci., 8, 2072-2084.
(8) Nozomi Nagano, Craig Porter & Janet Thornton (2001) The (βα)8 glycosidases: Sequence and structure analyses suggest distant evolutionary relationships. Protein Eng., 14, 845-855.
(9) Nozomi Nagano, Christine Orengo & Janet Thornton (2002) One fold with many functions - The evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321, 741-765.
(10) Nozomi Nagano. (2005). EzCatDB: The Enzyme Catalytic-Mechanism Database. Nucleic Acids Research, Molecular Biology Database on-line compilation 2005, 613, Online Journal
(11) Nozomi Nagano. (2005). EzCatDB: The Enzyme Catalytic-Mechanism Database. Nucleic Acids Research, 33 (1) Database Issue, D407-D412, Online Journal
(12) Nozomi Nagano, Tamotsu Noguchi, Yutaka Akiyama (2007) "Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database." PROTEINS: Structure, Function, and Bioinformatics. 66, 147-159.
(13) Chioko Nagao,Nozomi Nagano,Kenji Mizuguchi, (2010) "Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies." PROTEINS: Structure, Function, and Bioinformatics. 78, 2369-2384.