2YEQ

Structure of PhoD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Bacillus Subtilis Phosphodiesterase Phod Reveals an Iron and Calcium-Containing Active Site.

Rodriguez, F.Lillington, J.Johnson, S.Timmel, C.R.Lea, S.M.Berks, B.C.

(2014) J.Biol.Chem. 289: 30889

  • DOI: 10.1074/jbc.M114.604892

  • 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 pre ...

    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.


    Organizational Affiliation

    From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALKALINE PHOSPHATASE D
A, B
527Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: phoD (ycbS)
EC: 3.1.3.1
Find proteins for P42251 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42251
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PE5
Query on PE5

Download SDF File 
Download CCD File 
A, B
3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL, POLYETHYLENE GLYCOL PEG400
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 147.318α = 90.00
b = 147.318β = 90.00
c = 347.646γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
AutoPROCdata reduction
AutoPROCdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references, Structure summary
  • Version 1.2: 2014-11-19
    Type: Database references