Searching for amino acid sequence motifs among enzymes

The enzyme-reaction database

Mikita Suyama, Atsushi Ogiwara, Takaaki Nishioka, Jun'ichi Oda

Research output: Contribution to journalArticle

14 Citations (Scopus)

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 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.

Original languageEnglish
Pages (from-to)9-15
Number of pages7
JournalBioinformatics
Volume9
Issue number1
DOIs
Publication statusPublished - Feb 1 1993

Fingerprint

Amino Acid Motifs
Amino Acid Sequence
Amino acids
Enzymes
Databases
Amino Acids
Conserved Sequence
asparagine synthetase (glutamine-hydrolyzing)
Aspartate-Ammonia Ligase
Argininosuccinate Synthase
Chemical Databases
Chemical compounds
Glutamine
Names
Ligands
Multiplication
Fragment

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Searching for amino acid sequence motifs among enzymes : The enzyme-reaction database. / Suyama, Mikita; Ogiwara, Atsushi; Nishioka, Takaaki; Oda, Jun'ichi.

In: Bioinformatics, Vol. 9, No. 1, 01.02.1993, p. 9-15.

Research output: Contribution to journalArticle

Suyama, Mikita ; Ogiwara, Atsushi ; Nishioka, Takaaki ; Oda, Jun'ichi. / Searching for amino acid sequence motifs among enzymes : The enzyme-reaction database. In: Bioinformatics. 1993 ; Vol. 9, No. 1. pp. 9-15.
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