Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation

Motonori Ota, Kengo Kinoshita, Ken Nishikawa

Research output: Contribution to journalArticlepeer-review

76 Citations (Scopus)

Abstract

The catalytic or functionally important residues of a protein are known to exist in evolutionarily constrained regions. However, the patterns of residue conservation alone are sometimes not very informative, depending on the homologous sequences available for a given query protein. Here, we present an integrated method to locate the catalytic residues in an enzyme from its sequence and structure. Mutations of functional residues usually decrease the activity, but concurrently often increase stability. Also, catalytic residues tend to occupy partially buried sites in holes or clefts on the molecular surface. After confirming these general tendencies by carrying out statistical analyses on 49 representative enzymes, these data together with amino acid conservation were evaluated. This novel method exhibited better sensitivity in the prediction accuracy than traditional methods that consider only the residue conservation. We applied it to some so-called "hypothetical" proteins, with known structures but undefined functions. The relationships among the catalytic, conserved, and destabilizing residues in enzymatic proteins are discussed.

Original languageEnglish
Pages (from-to)1053-1064
Number of pages12
JournalJournal of Molecular Biology
Volume327
Issue number5
DOIs
Publication statusPublished - 2003 Apr 11
Externally publishedYes

Keywords

  • 3D profile
  • Desolvation
  • Hypothetical protein
  • K-nearest neighbor
  • Structural genomics

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Fingerprint Dive into the research topics of 'Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation'. Together they form a unique fingerprint.

Cite this