1H2E

BACILLUS STEAROTHERMOPHILUS PHOE (previously known as yhfr) in complex with phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Phosphate and Trivanadate Complexes of Bacillus Stearothermophilus Phosphatase Phoe: Structural and Functional Analysis in the Cofactor-Dependent Phosphoglycerate Mutase Superfamily

Rigden, D.J.Littlejohn, J.E.Henderson, K.Jedrzejas, M.J.

(2003) J.Mol.Biol. 325: 411

  • Primary Citation of Related Structures:  1H2F

  • PubMed Abstract: 
  • Bacillus stearothermophilus phosphatase PhoE is a member of the cofactor-dependent phosphoglycerate mutase superfamily possessing broad specificity phosphatase activity. Its previous structural determination in complex with glycerol revealed probable ...

    Bacillus stearothermophilus phosphatase PhoE is a member of the cofactor-dependent phosphoglycerate mutase superfamily possessing broad specificity phosphatase activity. Its previous structural determination in complex with glycerol revealed probable bases for its efficient hydrolysis of both large, hydrophobic, and smaller, hydrophilic substrates. Here we report two further structures of PhoE complexes, to higher resolution of diffraction, which yield a better and thorough understanding of its catalytic mechanism. The environment of the phosphate ion in the catalytic site of the first complex strongly suggests an acid-base catalytic function for Glu83. It also reveals how the C-terminal tail ordering is linked to enzyme activation on phosphate binding by a different mechanism to that seen in Escherichia coli phosphoglycerate mutase. The second complex structure with an unusual doubly covalently bound trivanadate shows how covalent modification of the phosphorylable His10 is accompanied by small structural changes, presumably to catalytic advantage. When compared with structures of related proteins in the cofactor-dependent phosphoglycerate mutase superfamily, an additional phosphate ligand, Gln22, is observed in PhoE. Functional constraints lead to the corresponding residue being conserved as Gly in fructose-2,6-bisphosphatases and Thr/Ser/Cys in phosphoglycerate mutases. A number of sequence annotation errors in databases are highlighted by this analysis. B. stearothermophilus PhoE is evolutionarily related to a group of enzymes primarily present in Gram-positive bacilli. Even within this group substrate specificity is clearly variable highlighting the difficulties of computational functional annotation in the cofactor-dependent phosphoglycerate mutase superfamily.


    Related Citations: 
    • A Cofactor-Dependent Phosphoglycerate Mutase Homolog from Bacillus Stearothermophilus is Actually a Broad Specificity Phosphatase
      Rigden, D.J.,Bagyan, I.,Lamani, E.,Setlow, P.,Jedrzejas, M.J.
      (2001) Protein Sci. 10: 1835
    • Structure and Mechanism of Action of a Cofactor-Dependent Phosphoglycerate Mutase Homolog from Bacillus Stearothermophilus with Broad Specificity Phosphatase Activity
      Rigden, D.J.,Mello, L.V.,Setlow, P.,Jedrzejas, M.J.
      (2002) J.Mol.Biol. 315: 1129


    Organizational Affiliation

    National Centre of Genetic Resources and Biotechnology, Cenargen/Embrapa, SAIN Parque Rural, Final W5, Asa Norte, 70770-900 Brasília, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATASE
A
207Geobacillus stearothermophilusGene Names: yhfR
Find proteins for Q9ALU0 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9ALU0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.546α = 90.00
b = 55.546β = 90.00
c = 164.645γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance