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

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.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Ota M,Kinoshita K,Nishikawa K

doi

10.1016/s0022-2836(03)00207-9

keywords:

subject

Has Abstract

pub_date

2003-04-11 00:00:00

pages

1053-64

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022283603002079

journal_volume

327

pub_type

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