Searching for amino acid sequence motifs among enzymes: the Enzyme-Reaction Database

Recently we have constructed a database—the Enzyme–ReactionDatabase–which links a chemical structure to amino acidsequences of enzymes that recognize the chemical structure astheir ligand. The total number of enzymes registered in thedatabase is 1103 with 6668 NBRF–PIR entry codes and 1756chemical compounds. The chemical structures and chemical namesfor 842 compounds are registered in the Chemical–StructureDatabase on the MACCS system. For each enzyme, the sequenceswere divided into clusters, and multiply aligned in each clusterto extract a conserved sequence. A total of 158 781 five–residue–longfragments were constructed from 433 conserved sequences andcompared among different clusters of different enzymes. Oneof these motifs shared by different enzymes S–G–G–L–D.The motif was conserved in both argininosuccinate synthase (EC6.3.4.5[EC]) and asparagine synthase (glutamine–hydrolysing)(EC 6.3.5.4[EC]). This result showed that the database was usefulfor the analysis of the relationship between chemical structuresand amino acid sequence motifs.