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

Authors
  • Suyama, M
  • Ogiwara, A
  • Nishioka, T
  • Oda, J
Type
Published Article
Journal
Computer applications in the biosciences : CABIOS
Publication Date
Feb 01, 1993
Volume
9
Issue
1
Pages
9–15
Identifiers
PMID: 8435774
Source
Medline
License
Unknown

Abstract

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.

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