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EzCatDB


NAR Molecular Biology Database Collection entry number 613
Nagano N.1, Nakagawa Z.2, Arita M.3,4, Tsukamoto K.1 and Noguchi T.1
1Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064 Japan
2Japan Industrial Technology Association (JITA), Tsukuba Office, Chuou 4th Office 4-10, 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-0046, Japan
3Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan
4Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan

Database Description

EzCatDB is a knowledge base that mainly includes enzyme reactions, in terms of sequences and tertiary structures of enzymes, and proposed catalytic mechanisms, as well as ligand structures. The EzCatDB provides a hierarchical classification of catalytic reactions, RLCP, which has considered catalytic mechanisms and active-site structures of enzymes as well as basic reactions and reactive parts of ligand molecules, along with literature information on structure and catalytic mechanisms. The EzCatDB clusters enzyme data in the Protein Data Bank and the Swiss-prot database with the same domain compositions and the same E.C. numbers and identical catalytic mechanisms. Furthermore, the EzCatDB provides ligand annotation of PDB data. For some enzyme entries, three-dimensional catalytic mechanisms, which are modeled from PDB data on the basis of the proposed mechanism reported in the literature, can be viewed with a Java-based viewer programme, 3D-EzCat, which adopts java3D as a Graphic Library. The EzCatDB can be queried according to the type of catalytic residue, name or type of ligand molecule that interacts with the enzyme as a cofactor, substrate, or product, in addition to literature information and the Swiss-prot accession number, PDB code and E.C. number. The EzCatDB is available at http://mbs.cbrc.jp/EzCatDB/ .

Recent Developments

Although RLCP classification had previously provided only hydrolysis, phosphorolysis and transfer reactions, it has come to include other reaction types such as addition, elimination and isomerization, which involve double bonds. Moreover, the database has been improved considerably to include classification of the catalytic domain, CatDom, compound list, E.C. classification and Swiss-prot entry list. For the 3D-EzCat viewer, the JOGL version was also developed in addition to the Java3D version, in order to speed up the viewer motions.

Acknowledgements

We would like to thank Yuko Hasegawa, Keitarou Nonaka, Kenji Morita, Munehiro Sugiyama, Junko Some, Mayumi Hisanaga and Fuyan Sun, who assisted in the annotation of enzyme data and collection of the literature. This project was supported by grants from PRESTO and BIRD, which have been organized by the Japan Science and Technology Corporation (JST), and from a Grant-in-Aid for Scientific Research (B) and a Grant-in-Aid for Publication of Scientific Research Results, which have been organized by the Japan Society for the Promotion of Science (JSPS).

References

1. Nagano N. (2005). EzCatDB: The Enzyme Catalytic-Mechanism Database. Nucleic Acids Res., 33: 407-412.
2. Nagano N, Noguchi T, Akiyama Y. (2007) Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database. PROTEINS: Structure, Function, and Bioinformatics. in press.

Subcategory: Protein structure

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