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. 2025 Jun;93(6):1181-1188.
doi: 10.1002/prot.26800. Epub 2025 Jan 22.

Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme

Nakia Polidori  1   2 , Peter Babin  1 , Bastian Daniel  1 , Karl Gruber  1
Affiliations

Structure, Oligomerization, and Thermal Stability of a Recently Discovered Old Yellow Enzyme

Nakia Polidori et al. Proteins. 2025 Jun.

Abstract

The Old Yellow Enzyme from Ferrovum sp. JA12 (FOYE) displays an unusual thermal stability for an enzyme isolated from a mesophilic organism. We determined the crystal structure of this enzyme and performed bioinformatic characterization to get insights into its thermal stability. The enzyme displays a tetrameric quaternary structure; however, unlike the other tetrameric homologs, it clusters in a separate phylogenetic group and possesses unique interactions that stabilize this oligomeric state. The thermal stability of this enzyme is mainly due to an unusually high number of intramolecular hydrogen bonds. Finally, this study provides a general analysis of the forces driving the oligomerization in Old Yellow Enzymes.

Keywords: ene‐reductase; old Yellow enzymes; oligomerization; oxidoreductase; thermophilic enzymes; thermostability.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

SCHEME 1
SCHEME 1
General reaction mechanism of Old Yellow Enzymes, divided into reductive and oxidative half‐reactions.
FIGURE 1
FIGURE 1
Unrooted tree of OYE structures present on the Protein Data Bank. Classification is based on the work of Peters et al. [12]. FOYE has a tetrameric structure.
FIGURE 2
FIGURE 2
FOYE tetramer, with the two functional dimers highlighted in orange and slate blue.
FIGURE 3
FIGURE 3
(a) FOYE tetramer (orange) compared to the ones from TOYE (blue), GkOYE (cyan), and Yqjm (purple). (b) Detail on the distortion of helix 7, promoting the tetramerization in FOYE.
FIGURE 4
FIGURE 4
(a) Active site of FOYE, with the conserved histidine residues (H177, H180) and the catalytic tyrosine (Y182) showed as sticks. The typical Class II cysteine residue (C25) is displayed as well. FMN is displayed in yellow. The C‐terminal from the other protomer, with the typical arginine finger (R352) is shown in orange. (b) Unstructured insertion in loop L3 (light green). FOYE thermal stability depends on an elevated number of hydrogen bonds.
FIGURE 5
FIGURE 5
Hydrogen bonds, salt bridges, and proline count in the four tetrameric Old Yellow Enzymes (FOYE, Yqjm, GkOYE, and TOYE) and the closest crystallized homolog of FOYE (RmER).
See this image and copyright information in PMC

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