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Related Experiment Video

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Defining Substrate Specificities for Lipase and Phospholipase Candidates
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Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.

Dorota Matelska1,2, Ivan G Shabalin1,3, Jagoda Jabłońska2

  • 1Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA.

BMC Evolutionary Biology
|December 23, 2018
PubMed
Summary

A new classification of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) reveals 22 subfamilies, including 13 novel ones. This phylogenetic analysis aids in understanding enzyme evolution and predicting functions for uncharacterized 2HADHs.

Keywords:
D-isomer specific 2-hydroxyacid dehydrogenasesMolecular evolutionSequence-structure-function relationshipSubstrate promiscuitySubstrate specificity

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Area of Science:

  • Biochemistry
  • Enzymology
  • Bioinformatics

Background:

  • D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) are oxidoreductases with diverse metabolic roles and biotechnological potential.
  • Sequence diversity and complex evolution complicate functional annotation of uncharacterized 2HADHs.

Purpose of the Study:

  • To perform an in-depth phylogenetic analysis of the 2HADHs family.
  • To revise the classification of 2HADHs based on evolutionary relationships.
  • To create a knowledgebase for exploring 2HADHs data and functional predictions.

Main Methods:

  • Phylogenetic analysis of 2HADHs sequences.
  • Mapping of existing biochemical and structural data onto the phylogenetic tree.
  • Aggregation of sequence, biochemical, and structural data for characterized subfamilies.

Main Results:

  • A revised classification of 2HADHs into 22 subfamilies, with 13 newly identified.
  • Identification of early divergence of subfamilies with broad substrate specificity.
  • Comprehensive data aggregation for nine biochemically studied subfamilies, detailing active sites and substrate recognition.

Conclusions:

  • The developed knowledgebase facilitates navigation, data searching, and functional prediction for 2HADHs.
  • Future research on novel subfamilies may uncover enzymes with new metabolic functions and biotechnological applications.