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Automatic assignment of reaction operators to enzymatic reactions.
Leber, Markus; Egelhofer, Volker; Schomburg, Ida; Schomburg, Dietmar.
Afiliación
  • Leber M; Institute for Biochemistry, University of Cologne, Zülpicher Strasse 47, Germany.
Bioinformatics ; 25(23): 3135-42, 2009 Dec 01.
Article en En | MEDLINE | ID: mdl-19783831
ABSTRACT

BACKGROUND:

Enzymes are classified in a numerical classification scheme introduced by the Nomenclature Committee of the IUBMB based on the overall reaction chemistry. Due to the manifold of enzymatic reactions the system has become highly complex. Assignment of enzymes to the enzyme classes requires a detailed knowledge of the system and manual analysis. Frequently rearrangements and deletions of enzymes and sub-subclasses are necessary.

RESULTS:

We use the Dugundji-Ugi model for coding of biochemical reactions which is based on electron shift patterns occurring during reactions. Changes of the bonds or of non-bonded valence electrons are expressed by reaction matrices. Our program calculates reaction matrices automatically on the sole basis of substrate and product chemical structures based on a new strategy for maximal common substructure determination, which allows an accurate atom mapping of the substrate and product atoms. The system has been tested for a large set of enzymatic reactions including all sub-subclasses of the EC classification system. Altogether 147 different representative reaction operators were found in the classified enzymes, 121 of which are unique with respect to an EC sub-subclass. The other 26 comprise groups of enzymes with very similar reactions, being identical with respect to the bonds formed and broken.

CONCLUSION:

The analysis and comparison of enzymatic reactions according to their electron shift patterns is defining enzyme groups characterised by unique reaction cores. Our results demonstrate the applicability of the Dugundji-Ugi model as a reasonable pre-classification system allowing an objective and rational view on biochemical reactions.

AVAILABILITY:

The program to generate reaction matrix descriptors is available upon request.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Biología Computacional / Enzimas Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2009 Tipo del documento: Article País de afiliación: Alemania

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Biología Computacional / Enzimas Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2009 Tipo del documento: Article País de afiliación: Alemania