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Related Experiment Videos

Short-chain dehydrogenases/reductases (SDRs).

Yvonne Kallberg1, Udo Oppermann, Hans Jörnvall

  • 1Department of Medical Biochemistry and Biophysics and Stockholm Bioinformatics Centre, Karolinska Institutet, Sweden.

European Journal of Biochemistry
|September 17, 2002
PubMed
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This study introduces a new functional assignment scheme for short-chain dehydrogenases/reductases (SDRs) based on sequence motifs. The scheme classifies SDRs into five families, predicting coenzyme preference and aiding functional analysis across diverse species.

Area of Science:

  • Biochemistry
  • Enzymology
  • Bioinformatics

Background:

  • Short-chain dehydrogenases/reductases (SDRs) exhibit significant functional diversity despite low sequence identities.
  • Common folding patterns and detectable sequence motifs exist within the SDR superfamily.
  • Existing classification schemes for SDRs require refinement.

Purpose of the Study:

  • To develop a novel functional assignment scheme for SDRs based on conserved sequence motifs.
  • To classify SDRs into distinct families and subfamilies.
  • To predict coenzyme specificities (NAD(H) vs. NADP(H)) for different SDR groups.

Main Methods:

  • Analysis of conserved sequence motifs within the SDR superfamily.
  • Development of a functional assignment scheme.

Related Experiment Videos

  • Application of the scheme to genomic data from human, mouse, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Saccharomyces cerevisiae.

    • Main Results:

    • Identified five SDR families: 'classical', 'extended', 'intermediate', 'divergent', and 'complex'.
    • Distinguished seven subfamilies of classical SDRs and three of extended SDRs, linking them to coenzyme preferences (NADP(H) for classical, NAD(H) for extended).
    • Demonstrated that primary structure alone is sufficient for functional assignment and coenzyme preference prediction in SDRs.

    Conclusions:

    • The developed motif-based scheme effectively classifies SDRs, revealing novel families and subfamilies.
    • Coenzyme preference can be accurately predicted from sequence motifs, aiding functional annotation.
    • The scheme provides a robust framework for understanding SDR diversity and function across different organisms.