title: Crystal structure of the Bacillus subtilis phosphodiesterase PhoD reveals an iron and calcium-containing active site.
abstract: The PhoD family of extra-cytoplasmic phosphodiesterases are among the most commonly occurring bacterial phosphatases. The exemplars for this family are the PhoD protein of Bacillus subtilis and the phospholipase D of Streptomyces chromofuscus. We present the crystal structure of B. subtilis PhoD. PhoD is most closely related to purple acid phosphatases (PAPs) with both types of enzyme containing a tyrosinate-ligated Fe(3+) ion. However, the PhoD active site diverges from that found in PAPs and uses two Ca(2+) ions instead of the single extra Fe(2+), Mn(2+), or Zn(2+) ion present in PAPs. The PhoD crystals contain a phosphate molecule that coordinates all three active site metal ions and that is proposed to represent a product complex. A C-terminal helix lies over the active site and controls access to the catalytic center. The structure of PhoD defines a new phosphatase active site architecture based on Fe(3+) and Ca(2+) ions.
authors.affiliation: From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU.
authors.forename: Fernanda
authors.initials: F
authors.lastname: Rodriguez
authors.affiliation: the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and the Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.
authors.forename: James
authors.initials: J
authors.lastname: Lillington
authors.affiliation: the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and.
authors.forename: Steven
authors.initials: S
authors.lastname: Johnson
authors.affiliation: the Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.
authors.forename: Christiane R
authors.initials: CR
authors.lastname: Timmel
authors.affiliation: the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and susan.lea@path.ox.ac.uk.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Lea
authors.affiliation: From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, ben.berks@bioch.ox.ac.uk.
authors.forename: Ben C
authors.initials: BC
authors.lastname: Berks
mesh_terms: D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry*; D002118:Calcium / Q000737:chemistry; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004578:Electron Spin Resonance Spectroscopy; D006863:Hydrogen-Ion Concentration; D007501:Iron / Q000737:chemistry; D008024:Ligands; D008670:Metals / Q000737:chemistry; D008969:Molecular Sequence Data; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry*; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D014443:Tyrosine / Q000737:chemistry; D015032:Zinc / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D008670:Metals; D014443:Tyrosine; D007501:Iron; D010744:Phosphoric Monoester Hydrolases; D010727:Phosphoric Diester Hydrolases; D015032:Zinc; D002118:Calcium
keywords: Bacterial Metabolism; Catalysis; Metalloenzyme; Phosphatase; Structural Biology