Structural Insights into the UbiD Protein Family from the Crystal Structure of PA0254 from Pseudomonas aeruginosa

Abstract

The 3-polyprenyl-4-hydroxybenzoate decarboxylase (UbiD) catalyzes the conversion of 3-polyprenyl-4-hydroxybenzoate to 2-polyprenylphenol in the biosynthesis of ubiquinone. Pseudomonas aeruginosa contains two genes (PA0254 and PA5237) that are related in sequence to putative UbiD enzymes. A bioinformatics analysis suggests that the UbiD sequence family can be divided into two subclasses, with PA5237 and PA0254 belonging to different branches of this family. The three-dimensional structure of PA0254 has been determined using single wavelength anomalous diffraction and molecular replacement in two different crystal forms to resolutions of 1.95 and 2.3 Å, respectively. The subunit of PA0254 consists of three domains, an N-terminal α/β domain, a split β-barrel with a similar fold of a family of flavin reductases and a C-terminal α/β domain with a topology characteristic for the UbiD protein family. The middle domain contains a metal binding site adjacent to a large open cleft that may represent the active site. The two protein ligands binding a magnesium ion, His188 and Glu229, invariant in the PA0254 subclass, are also conserved in a corresponding metal site found in one of the FMN binding proteins from the split β-barrel fold family. PA0254 forms, in contrast to the hexameric UbiD from E. coli and P. aeruginosa, a homo-dimer. Insertion of four residues in a loop region in the PA0254 type enzymes results in structural differences that are incompatible with hexamer assembly.

Isofunctional Enzymes PAD1 and UbiX Catalyze Formation of a Novel Cofactor Required by Ferulic Acid Decarboxylase and 4-Hydroxy-3-polyprenylbenzoic Acid Decarboxylase

“…The UbiD enzymes comprise three domains, and it is particularly intriguing that the central domain possesses a split β-barrel fold characteristic of flavinreductases. 15 The structures reveal a large cleft in the putative flavin-binding domain that could potentially accommodate FMN or a modified FMN derivative. We speculate that under the conditions used to overexpress these enzymes for crystallographic analysis, endogenous UbiX could not synthesize sufficient cofactor to saturate UbiD and that the cofactor may also have been lost or degraded during purification.…”

Phthaloyl‐coenzyme A decarboxylase from Thauera chlorobenzoica: the prenylated flavin‐, K+‐ and Fe2+‐dependent key enzyme of anaerobic phthalate degradation

“…UbiD‐like enzymes have been reported to contain divalent cations (Jacewicz et al ., ; Payne et al ., ; Marshall et al ., ). ICP‐MS analysis of PCD revealed 1.8 ± 0.2 (mean of three replicates ± standard deviations) mol Fe per mol enzyme, while for Mn, Co, Ni, Cu, Zn, Mo, Mg and Ca the values obtained were either below the detection limit and/or not significantly different from the buffer blanks.…”

Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae

“…Structural studies of phenol acid decarboxylases define the following three general types of this enzyme: (i) dodecameric, UbiXtype flavoproteins (23,24); (ii) the microbial lipocalin-related phenylacrylic acid decarboxylases (27)(28)(29); and (iii) the UbiD-like enzymes (30). The X-ray crystal structure of yeast FDC1 clearly establishes this enzyme as a member of the UbiD family of decarboxylases ( Fig.…”

“…A third type of decarboxylase was identified in the UbiD-related putative 3-polyprenyl-4-hydroxybenzoate decarboxylase from Pseudomonas aeruginosa PA0254 (30). The UbiD-related proteins from P. aeruginosa function as either dimeric or hexameric proteins composed of 50-kDa monomers (30). As with UbiX, UbiD proteins are thought to function in ubiquinone biosynthesis (31); however, the metabolic relationship between these two proteins is unclear.…”