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A functional-phylogenetic classification system for transmembrane solute transporters.

M H Saier1

  • 1Department of Biology, University of California at San Diego, La Jolla, California 92093-0116, USA. msaier@ucsd.edu

Microbiology and Molecular Biology Reviews : MMBR
|June 6, 2000
PubMed
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A new classification system for molecular transporters, based on transport mode, energy coupling, and phylogenetic families, aids in identifying transporter functions. This system helps assign roles to newly discovered transport proteins from genome sequencing projects.

Area of Science:

  • Biochemistry and Molecular Biology
  • Membrane Transport
  • Protein Classification

Background:

  • A comprehensive classification system for transmembrane molecular transporters has been established.
  • This system was approved by the International Union of Biochemistry and Molecular Biology nomenclature committee's transport panel.
  • It categorizes over 250 transporter families based on defined criteria.

Purpose of the Study:

  • To present a newly developed, comprehensive classification system for transmembrane molecular transporters.
  • To provide a framework for understanding transporter structure, function, and evolutionary relationships.
  • To facilitate the assignment of functions to newly identified transport proteins.

Main Methods:

  • Classification based on transporter class/subclass (transport mode, energy coupling), protein phylogenetic family/subfamily, and substrate specificity.

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  • Categorization into distinct groups: channels, secondary active transporters, primary active transporters, group translocators, and proteins of unknown function.
  • Cross-referencing of transporters by transport mode, energy coupling mechanism, phylogenetic grouping, and substrates.

    • Main Results:

    • The classification system utilizes immutable characteristics (transport mode, energy coupling) as primary bases, phylogenetic grouping as a secondary basis, and substrate specificity as a tertiary basis.
    • Identified categories include 115 channel families, 78 secondary active transporter families, 23 primary active transporter families, 6 group translocator families, and 51 families of unknown function.
    • Phylogenetic families generally share a single transport mode and energy coupling mechanism, accommodating diverse substrates.

    Conclusions:

    • The developed classification system provides a robust framework for organizing and understanding transmembrane molecular transporters.
    • It aids in the familial and functional assignment of newly sequenced transport proteins.
    • The system highlights the evolutionary conservation of transport mechanisms within phylogenetic families.