An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations

Abstract

The group of proteins that contain a thioredoxin (Trx) fold is huge and diverse. Assessment of the variation in catalytic machinery of Trx fold proteins is essential in providing a foundation for understanding their functional diversity and predicting the function of the many uncharacterized members of the class. The proteins of the Trx fold class retain common features—including variations on a dithiol CxxC active site motif—that lead to delivery of function. We use protein similarity networks to guide an analysis of how structural and sequence motifs track with catalytic function and taxonomic categories for 4,082 representative sequences spanning the known superfamilies of the Trx fold. Domain structure in the fold class is varied and modular, with 2.8% of sequences containing more than one Trx fold domain. Most member proteins are bacterial. The fold class exhibits many modifications to the CxxC active site motif—only 56.8% of proteins have both cysteines, and no functional groupings have absolute conservation of the expected catalytic motif. Only a small fraction of Trx fold sequences have been functionally characterized. This work provides a global view of the complex distribution of domains and catalytic machinery throughout the fold class, showing that each superfamily contains remnants of the CxxC active site. The unifying context provided by this work can guide the comparison of members of different Trx fold superfamilies to gain insight about their structure-function relationships, illustrated here with the thioredoxins and peroxiredoxins.

A Novel Redoxin in the Thylakoid Membrane Regulates the Titer of Photosystem I

“…Trxs belong to the thioredoxin superfamily of proteins, which contain a common thioredoxin fold with a characteristic two-cysteine CXXC active site motif (where X is any amino acid). The CXXC motifs have different variants, including Trx folds with only a single cysteine, which are comparatively less well studied (3). Redox regulation by Trx fold proteins via their oxidation, reduction, or disulfide exchange activities, depending on their redox environments, is an extensive system in almost all life forms, including oxygenic photosynthetic organisms.…”

The Crystal Structure of the Protein-Disulfide Isomerase Family Member ERp27 Provides Insights into Its Substrate Binding Capabilities

“…The thioredoxin fold, named after the reductase thioredoxin A, is a protein architecture common to many oxidoreductases. The canonical fold is char-acterized by a central four-stranded ␤-sheet flanked by three ␣-helices (18) arranged in the secondary structure sequence ␤ 1 -␣ 1 -␤ 2 -␣ 2 -␤ 3 -␤ 4 -␣ 3 , which in some proteins is extended at the N terminus by an extra ␤-strand and ␣-helix, resulting in a ␤ 0 -␣ 0 -␤ 1 -␣ 1 -␤ 2 -␣ 2 -␤ 3 -␤ 4 -␣ 3 sequence (19). Most well characterized members of the PDI family also contain the thioredoxin active site motif WCXXCK (20) located at the N terminus of the ␣ 1 -helix, which can facilitate the catalysis of both cysteine oxidation and disulfide bond isomerization.…”

Protein Based Drug Discovery

“…Only a small fraction of Trx fold sequences have been functionally characterized. Unifying context provided by work can guide the comparison of members of different Trx fold superfamilies to gain insight about their structure-function relationships, illustrated here with the thioredoxins and peroxiredoxins [30]. Proteomic analysis occupies an increasingly important place in gamete and embryo biology as an independent tool of discovery and as a means of follow-up to transcriptional profiling.…”