The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form.

Eva Kyslíková,Jiří Zahradník,Jaroslav Nunvar,Bohdan Schneider,Michal Grulich,Jiří Černý,Pavel Kyslík,Miroslav Šulc,Petr Kolenko,Andrea Palyzová,Helena Marešová,Lucie Kolářová

doi:10.1371/journal.pone.0195299

Abstract

Old Yellow Enzymes (OYEs) are NAD(P)H dehydrogenases of not fully resolved physiological roles that are widespread among bacteria, plants, and fungi and have a great potential for biotechnological applications. We determined the apo form crystal structure of a member of the OYE class, glycerol trinitrate reductase XdpB, from Agrobacterium bohemicum R89-1 at 2.1 Å resolution. In agreement with the structures of the related bacterial OYEs, the structure revealed the TIM barrel fold with an N-terminal β-hairpin lid, but surprisingly, the structure did not contain its cofactor FMN. Its putative binding site was occupied by a pentapeptide TTSDN from the C-terminus of a symmetry related molecule. Biochemical experiments confirmed a specific concentration-dependent oligomerization and a low FMN content. The blocking of the FMN binding site can exist in vivo and regulates enzyme activity. Our bioinformatic analysis indicated that a similar self-inhibition could be expected in more OYEs which we designated as subgroup OYE C1. This subgroup is widespread among G-bacteria and can be recognized by the conserved sequence GxxDYP in proximity of the C termini. In proteobacteria, the C1 subgroup OYEs are typically coded in one operon with short-chain dehydrogenase. This operon is controlled by the tetR-like transcriptional regulator. OYEs coded in these operons are unlikely to be involved in the oxidative stress response as the other known members of the OYE family because no upregulation of XdpB was observed after exposing A. bohemicum R89-1 to oxidative stress.

Highlights

Members of the Old Yellow Enzyme family (OYEs) are NAD(P)H dehydrogenases containing noncovalently bound flavin-mononucleotide (FMN)
A characteristic feature of Old Yellow Enzymes (OYEs) is the β-hairpin lid formed by the N-terminal amino acids and a well conserved FMN binding site formed by the C-terminal edges of the β-barrel
The cultures of bacteria were grown in an LB medium (1.0% tryptone, 0.5% yeast extract, 1.0% sodium chloride; pH 7.0 adjusted before sterilization) or in an expression LB medium supplemented with trace elements—LBTE (TE: MgSO4.7H2O 200 mg.l-1, CaCl2.2H2O 50 mg.l-1 and FeSO4.7H2O 10 mg.l-1)

Summary

Introduction

Members of the Old Yellow Enzyme family (OYEs) are NAD(P)H dehydrogenases containing noncovalently bound flavin-mononucleotide (FMN). These enzymes have been reported in bacteria, yeasts, fungi, plants, invertebrates, and rarely in higher animals. OYEs 3D structures adopt the highly conserved (αβ) TIM-barrel fold with a closed, central β-barrel. A characteristic feature of OYEs is the β-hairpin lid formed by the N-terminal amino acids and a well conserved FMN binding site formed by the C-terminal edges of the β-barrel.

Methods

Results

Conclusion