Structural Classification of Thioredoxin-Like Fold Proteins

Proteins. 2005 Feb 1;58(2):376-88. doi: 10.1002/prot.20329.

Abstract

Protein structure classification is necessary to comprehend the rapidly growing structural data for better understanding of protein evolution and sequence-structure-function relationships. Thioredoxins are important proteins that ubiquitously regulate cellular redox status and various other crucial functions. We define the thioredoxin-like fold using the structure consensus of thioredoxin homologs and consider all circular permutations of the fold. The search for thioredoxin-like fold proteins in the PDB database identified 723 protein domains. These domains are grouped into eleven evolutionary families based on combined sequence, structural, and functional evidence. Analysis of the protein-ligand structure complexes reveals two major active site locations for the thioredoxin-like proteins. Comparison to existing structure classifications reveals that our thioredoxin-like fold group is broader and more inclusive, unifying proteins from five SCOP folds, five CATH topologies and seven DALI domain dictionary globular folding topologies. Considering these structurally similar domains together sheds new light on the relationships between sequence, structure, function and evolution of thioredoxins.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Bacillus / enzymology
  • Binding Sites
  • Chorismate Mutase / metabolism
  • Cytidine Deaminase / chemistry
  • Databases, Protein
  • Escherichia coli / enzymology
  • Evolution, Molecular
  • Humans
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Oxidation-Reduction
  • Protein Binding
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / chemistry
  • Proteomics / methods*
  • Sequence Homology, Amino Acid
  • Structure-Activity Relationship
  • Thioredoxins / chemistry*

Substances

  • Ligands
  • Proteins
  • Thioredoxins
  • Cytidine Deaminase
  • Chorismate Mutase