Searching for amino acid sequence motifs among enzymes: the Enzyme-Reaction Database.
Recently we have constructed a database--the Enzyme-Reaction Database--which links a chemical structure to amino acid sequences of enzymes that recognize the chemical structure as their ligand. The total number of enzymes registered in the database is 1103 with 6668 NBRF-PIR entry codes and 1756 chemical compounds. The chemical structures and chemical names for 842 compounds are registered in the Chemical-Structure Database on the MACCS system. For each enzyme, the sequences were divided into clusters, and multiply aligned in each cluster to extract a conserved sequence. A total of 158,781 five-residue-long fragments were constructed from 433 conserved sequences and compared among different clusters of different enzymes. One of these motifs shared by different enzymes was S-G-G-L-D. The motif was conserved in both argininosuccinate synthase (EC 6.3.4.5) and asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4). This result showed that the database was useful for the analysis of the relationship between chemical structures and amino acid sequence motifs.
Suyama
M
M
Institute for Chemical Research, Kyoto University, Japan.
Ogiwara
A
A
Nishioka
T
T
Oda
J
J
D000465:Algorithms; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D003628:Database Management Systems; D004798:Enzymes / Q000737:chemistry* / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D012985:Software Design; D013329:Structure-Activity Relationship
D004798:Enzymes