Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7.
The crystal structure of the flavoprotein Pad1 from Escherichia coli O157:H7 complexed with the cofactor FMN has been determined by the multiple anomalous diffraction method and refined at 2.0 A resolution. This protein is a paralog of UbiX (3-octaprenyl-4-hydroxybenzoate carboxylyase, 51% sequence identity) that catalyzes the third step in ubiquinone biosynthesis and to Saccharomyces cerevisiae Pad1 (54% identity), an enzyme that confers resistance to the antimicrobial compounds phenylacrylic acids through decarboxylation of these compounds. Each Pad1 monomer consists of a typical Rossmann fold containing a non-covalently bound molecule of FMN. The fold of Pad1 is similar to MrsD, an enzyme associated with lantibiotic synthesis; EpiD, a peptidyl-cysteine decarboxylase; and AtHAL3a, the enzyme, which decarboxylates 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine during coenzyme A biosynthesis, all with a similar location of the FMN binding site at the interface between two monomers, yet each having little sequence similarity to one another. All of these proteins associate into oligomers, with a trimer forming the common structural unit in each case. In MrsD and EpiD, which belong to the homo-dodecameric flavin-containing cysteine decarboxylase (HFCD) family, these trimers associate further into dodecamers. Pad1 also forms dodecamers, although the association of the trimers is completely different, resulting in exposure of a different side of the trimer unit to the solvent. This exposure affects the location of the substrate binding site and, specifically, its access to the FMN cofactor. Therefore, Pad1 forms a separate family, distinguishable from the HFCD family.
Rangarajan
Erumbi S
ES
Biotechnology Research Institute, NRCC, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada.
Li
Yunge
Y
Iannuzzi
Pietro
P
Tocilj
Ante
A
Hung
Li-Wei
LW
Matte
Allan
A
Cygler
Miroslaw
M
D029681:Arabidopsis Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D002262:Carboxy-Lyases / Q000737:chemistry*; D018360:Crystallography, X-Ray; D019281:Dimerization; D019453:Escherichia coli O157 / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D005486:Flavin Mononucleotide / Q000737:chemistry; D005420:Flavoproteins / Q000737:chemistry; D040681:Structural Homology, Protein
D029681:Arabidopsis Proteins; C404262:AtHAL3 protein, Arabidopsis; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D005420:Flavoproteins; D005486:Flavin Mononucleotide; D002262:Carboxy-Lyases; C450426:MrsD protein, Bacillus; C087194:phenylacrylic acid decarboxylase; C113304:ubiX protein, E coli