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Related Experiment Videos

Structural classification of thioredoxin-like fold proteins.

Yuan Qi1, Nick V Grishin

  • 1Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA.

Proteins
|November 24, 2004
PubMed
Summary

This study defines the thioredoxin-like fold, identifying 723 protein domains across eleven families. This classification broadens understanding of protein evolution and sequence-structure-function relationships.

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Area of Science:

  • Structural biology
  • Biochemistry
  • Evolutionary biology

Background:

  • Protein structure classification is crucial for understanding protein evolution and function.
  • Thioredoxins are vital proteins regulating cellular redox status and other functions.

Purpose of the Study:

  • To define the thioredoxin-like fold, including circular permutations.
  • To identify and classify thioredoxin-like proteins in the Protein Data Bank (PDB).
  • To analyze active site locations and compare with existing classifications.

Main Methods:

  • Defined thioredoxin-like fold using structure consensus of homologs.
  • Searched the PDB database for thioredoxin-like fold proteins.
  • Grouped identified domains into evolutionary families using sequence, structural, and functional data.

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  • Analyzed protein-ligand complexes and compared with SCOP, CATH, and DALI classifications.

    • Main Results:

    • Identified 723 protein domains with a thioredoxin-like fold.
    • Grouped these domains into eleven distinct evolutionary families.
    • Revealed two major active site locations within thioredoxin-like proteins.
    • Demonstrated that the defined thioredoxin-like fold is broader than existing classifications, unifying proteins from multiple databases.

    Conclusions:

    • The proposed thioredoxin-like fold classification is more inclusive, unifying diverse proteins.
    • This broader classification provides new insights into sequence-structure-function and evolutionary relationships.
    • Understanding these relationships is key to comprehending protein evolution and function.