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 
  • R-Value Observed: 0.180 

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
  • Primary Citation of Related Structures:  
    2YEQ

  • 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, ben.berks@bioch.ox.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALKALINE PHOSPHATASE DAB527Bacillus subtilisMutation(s): 0 
EC: 3.1.3.1
Find proteins for P42251 (Bacillus subtilis (strain 168))
Explore P42251 
Go to UniProtKB:  P42251
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE5
Query on PE5

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A, B
3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-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 
  • R-Value Observed: 0.180 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.318α = 90
b = 147.318β = 90
c = 347.646γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
AutoPROCdata reduction
AutoPROCdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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