1SBZ

Crystal Structure of dodecameric FMN-dependent Ubix-like Decarboxylase from Escherichia coli O157:H7

Summary for 1SBZ

• Entry DOI: 10.2210/pdb1sbz/pdb
• Descriptor: Probable aromatic acid decarboxylase, FLAVIN MONONUCLEOTIDE (3 entities in total)
• Functional Keywords: fmn binding, pad1, ubix, montreal-kingston bacterial structural genomics initiative, bsgi, structural genomics, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 89868.27

Authors

Rangarajan, E.S.,Li, Y.,Iannuzzi, P.,Tocilj, A.,Hung, L.-W.,Matte, A.,Cygler, M.,Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) (deposition date: 2004-02-11, release date: 2004-10-26, Last modification date: 2019-07-24)

Primary citation

Rangarajan, E.S.,Li, Y.,Iannuzzi, P.,Tocilj, A.,Hung, L.-W.,Matte, A.,Cygler, M.
Crystal structure of a dodecameric FMN-dependent UbiX-like decarboxylase (Pad1) from Escherichia coli O157: H7.
Protein Sci., 13:3006-3016, 2004

PubMed Abstract: 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.

PubMed: 15459342
DOI: 10.1110/ps.04953004

Experimental method

X-RAY DIFFRACTION (2 Å)