2YEQ

Structure of PhoD

Summary for 2YEQ

• Entry DOI: 10.2210/pdb2yeq/pdb
• Descriptor: ALKALINE PHOSPHATASE D, 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL, 1,2-ETHANEDIOL, ... (8 entities in total)
• Functional Keywords: hydrolase, phosphodiesterase
• Biological source: BACILLUS SUBTILIS
• Total number of polymer chains: 2
• Total formula weight: 134794.58

Authors

Lillington, J.E.D.,Rodriguez, F.,Roversi, P.,Johnson, S.J.,Berks, B.,Lea, S.M. (deposition date: 2011-03-30, release date: 2012-04-18, Last modification date: 2024-05-08)

Primary citation

Rodriguez, F.,Lillington, J.,Johnson, S.,Timmel, C.R.,Lea, S.M.,Berks, B.C.
Crystal Structure of the Bacillus Subtilis Phosphodiesterase Phod Reveals an Iron and Calcium-Containing Active Site.
J.Biol.Chem., 289:30889-, 2014

PubMed 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.

PubMed: 25217636
DOI: 10.1074/JBC.M114.604892

Experimental method

X-RAY DIFFRACTION (1.93 Å)