Enzymes database searches

Thus, the EC numbers provide unique identifiers for enzyme functions and give us useful keyword entries in database searches. 

SEARCH AND ANALYSIS OF ENZYME DATA 7.3.1. Search for Enzyme Database... 

Figure 7.5. Search enzyme information at Brenda. Brenda is the comprehensive enzyme database for retrieving chemical, kinetic, and structural properties of enzymes via EC number, enzyme name, and organism (biological source). The search page by EC number is shown.

Search enzyme databases for information to construct a database of glucosidases (EC 3.2.1.x) with retrievable fields on substrate (anomeric) specificity, catalytic mechanism (stereochemical, e.g., inversion versus retention) and kinetic constants (e.g., Km and V). 

Type 2 MTs, also currently understood to function exclusively as OMTs, are found in all lignin-producing plants. This family is specific for coenzyme A derivatized phenylpropanoid compounds and appears to be less diverse in sequence and gene number than the type 1 family of MTs (Fig. 2.3). Based on database searches, type 2 OMTs consist of caffeoyl and feruloyl coenzyme-A specific OMTs (CCoAOMTs). The most closely related enzymes to plant CCoAOMTs are the mammalian small molecule methyltransferases, including catechol OMT and bacterial MTs involved in macrolide biosynthesis. 

Because the three genes encoding the canonical members of this family -SAMT, BAMT, and JMT have only recently been characterized, the full extent of this family is not known. Database searches using the BLAST 2.0 program reveal a number of unknown gene products and putative SAMT -like enzymes as well as caffeine synthases belonging to the type 3 family of MTs. Thus, the family includes not only carboxyl methyltransferases but also some alkaloid N-methyltransferases. 

The ENZYME database (http //www.expasy.ch/enzyme/) provides basic information about specific enzymes. It is based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. In this database, you can obtain the EC number of any enzyme, its recommended name, alternative names, cofactors, and human diseases associated with the enzyme. You can trace the enzyme from its name to the reaction it catalyses—to the metabolic pathway(s) in which it participates—to the large and intricate Boehringer Mannheim Biochemical Pathways Wallchart. You also can search the database by metabolites or pathways. 

Database search parameters for the TOF/TOF data using the Mascot search engine Homo sapiens for taxonomy, NCBIr for database, no enzyme, no modifications, mass tolerance of the precursor ion at 0.2 kDa and the fragment ions at ... 

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