4BX2

Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosphatase) in complex with Beryllium trifluoride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.193 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Chronophin Dimerization is Required for Proper Positioning of its Substrate Specificity Loop.

Kestler, C.Knobloch, G.Tessmer, I.Jeanclos, E.Schindelin, H.Gohla, A.

(2014) J.Biol.Chem. 289: 3094

  • DOI: 10.1074/jbc.M113.536482
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mammalian phosphatases of the haloacid dehalogenase (HAD) superfamily have emerged as important regulators of physiology and disease. Many of these enzymes are stable homodimers; however, the role of their dimerization is largely unknown. Here, we ex ...

    Mammalian phosphatases of the haloacid dehalogenase (HAD) superfamily have emerged as important regulators of physiology and disease. Many of these enzymes are stable homodimers; however, the role of their dimerization is largely unknown. Here, we explore the function of the obligatory homodimerization of chronophin, a mammalian HAD phosphatase known to dephosphorylate pyridoxal 5'-phosphate (PLP) and serine/threonine-phosphorylated proteins. The exchange of two residues in the murine chronophin homodimerization interface (chronophin(A194K,A195K)) yields a constitutive monomer both in vitro and in cells. The catalytic activity of monomeric chronophin toward PLP is strongly impaired. X-ray crystallographic studies of chronophin(A194K,A195K) revealed that dimer formation is essential for an intermolecular arginine-arginine-tryptophan stacking interaction that positions a critical histidine residue in the substrate specificity loop of chronophin for PLP coordination. Analysis of all available crystal structures of HAD hydrolases that are grouped together with chronophin in the C2a-type structural subfamily uncovered a highly conserved mode of dimerization that results in intermolecular contacts involving the substrate specificity loop. Our results explain how the dimerization of HAD hydrolases contributes to their catalytic efficiency and substrate specificity.


    Organizational Affiliation

    From the Institute for Pharmacology and Toxicology, University of Würzburg, 97078 Würzburg, Germany and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRIDOXAL PHOSPHATE PHOSPHATASE
A, B
293Mus musculusMutation(s): 0 
Gene Names: Pdxp (Cin, Plp, Plpp)
EC: 3.1.3.3, 3.1.3.74
Find proteins for P60487 (Mus musculus)
Go to UniProtKB:  P60487
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, B
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.193 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 166.830α = 90.00
b = 166.830β = 90.00
c = 166.830γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references