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Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary

Yingfei Chen1, Daniel S Black2, Peter J Reilly3

  • 1Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011.

Protein Science : a Publication of the Protein Society
|August 18, 2016
PubMed
Summary

This study presents the first systematic structural classification of carboxylic ester hydrolases (CEHs), organizing them into 91 families and five clans based on structural similarities. The findings establish a comprehensive framework for understanding these important enzymes.

Keywords:
carboxylesterasescholinesterasescocaine esterasescutinaseslysopholipasesphospholipasestriacylglycerol lipases

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Carboxylic ester hydrolases (CEHs) are a diverse group of enzymes with crucial biological roles.
  • Previous classification efforts lacked a systematic structural basis.
  • Understanding CEH structural diversity is key to enzyme function and engineering.

Purpose of the Study:

  • To establish the first systematic structural classification of carboxylic ester hydrolases (CEHs).
  • To group CEHs into families and clans based on conserved structural features.
  • To create an accessible database for CEH structural information.

Main Methods:

  • Utilized multiple sequence alignments, secondary structure analysis, and tertiary structure superpositions for classification.
  • Employed the Basic Local Alignment Search Tool (BLAST) to gather CEHs from public databases.
  • Analyzed primary, secondary, and tertiary structures to define family and clan relationships.

Main Results:

  • Classified CEHs into 91 families, with 36 families grouped into five distinct clans.
  • Identified conserved active sites and reaction mechanisms within CEH families.
  • Characterized diverse tertiary structures including alpha/beta-hydrolase folds, beta-propellers, and helix bundles.
  • The CASTLE database was constructed, containing 321,830 primary and 1378 tertiary structures.

Conclusions:

  • The study provides a comprehensive and systematic structural classification of CEHs.
  • Structural similarities underpin the grouping of CEHs into families and clans, even with divergent primary sequences.
  • The CASTLE database serves as a valuable resource for researchers studying CEHs.