3NAD: Crystal Structure of Phenolic Acid Decarboxylase from Bacillus pumilus UI-670

The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavouring and polymer industries. Here, the crystal structure of phenolic acid decarboxylase (PAD) from Bacillus pumilus strain UI-670 is reported. The enzyme is a 161-residue polypeptide that forms dimers both in the crystal and in solution. The structure of PAD as determined by X-ray crystallography revealed a beta-barrel structure and two alpha-helices, with a cleft formed at one edge of the barrel. The PAD structure resembles those of the lipocalin-fold proteins, which often bind hydrophobic ligands. Superposition of structurally related proteins bound to their cognate ligands shows that they and PAD bind their ligands in a conserved location within the beta-barrel. Analysis of the residue-conservation pattern for PAD-related sequences mapped onto the PAD structure reveals that the conservation mainly includes residues found within the hydrophobic core of the protein, defining a common lipocalin-like fold for this enzyme family. A narrow cleft containing several conserved amino acids was observed as a structural feature and a potential ligand-binding site.
PDB ID: 3NADDownload
MMDB ID: 86109
PDB Deposition Date: 2010/6/1
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.69  Å
Source Organism:
Similar Structures:
Biological Unit for 3NAD: dimeric; determined by author and by software (PISA)
Molecular Components in 3NAD
Label Count Molecule
Proteins (2 molecules)
Ferulate Decarboxylase
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

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