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Structural classification of thioredoxin‐like fold proteins
Author(s) -
Qi Yuan,
Grishin Nick V.
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20329
Subject(s) - thioredoxin , protein data bank (rcsb pdb) , biology , protein folding , computational biology , protein structure , structural motif , structural similarity , protein family , sequence (biology) , threading (protein sequence) , protein data bank , protein function prediction , genetics , biochemistry , protein function , gene
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. Proteins 2005. © 2004 Wiley‐Liss, Inc.