4BKM

Crystal structure of the murine AUM (phosphoglycolate phosphatase) capping domain as a fusion protein with the catalytic core domain of murine chronophin (pyridoxal phosphate phosphatase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Evolutionary and Structural Analyses of the Mammalian Haloacid Dehalogenase-Type Phosphatases Aum and Chronophin Provide Insight Into the Basis of Their Different Substrate Specificities.

Seifried, A.Knobloch, G.Duraphe, P.S.Segerer, G.Manhard, J.Schindelin, H.Schultz, J.Gohla, A.

(2014) J.Biol.Chem. 289: 3416

  • DOI: 10.1074/jbc.M113.503359

  • PubMed Abstract: 
  • Mammalian haloacid dehalogenase (HAD)-type phosphatases are an emerging family of phosphatases with important functions in physiology and disease, yet little is known about the basis of their substrate specificity. Here, we characterize a previously ...

    Mammalian haloacid dehalogenase (HAD)-type phosphatases are an emerging family of phosphatases with important functions in physiology and disease, yet little is known about the basis of their substrate specificity. Here, we characterize a previously unexplored HAD family member (gene annotation, phosphoglycolate phosphatase), which we termed AUM, for aspartate-based, ubiquitous, Mg(2+)-dependent phosphatase. AUM is a tyrosine-specific paralog of the serine/threonine-specific protein and pyridoxal 5'-phosphate-directed HAD phosphatase chronophin. Comparative evolutionary and biochemical analyses reveal that a single, differently conserved residue in the cap domain of either AUM or chronophin is crucial for phosphatase specificity. We have solved the x-ray crystal structure of the AUM cap fused to the catalytic core of chronophin to 2.65 Å resolution and present a detailed view of the catalytic clefts of AUM and chronophin that explains their substrate preferences. Our findings identify a small number of cap domain residues that encode the different substrate specificities of AUM and chronophin.


    Organizational Affiliation

    From the Institute for Pharmacology and Toxicology.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
A, B, C, D
309Mus musculusMutation(s): 0 
Gene Names: Pgp, Pdxp (Cin, Plp, Plpp)
EC: 3.1.3.21 3.1.3.3, 3.1.3.74
Find proteins for Q8CHP8 (Mus musculus)
Go to UniProtKB:  Q8CHP8
Find proteins for P60487 (Mus musculus)
Go to UniProtKB:  P60487
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.500α = 90.00
b = 91.960β = 90.20
c = 105.920γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling

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: 2014-02-19
    Type: Database references
  • Version 1.2: 2017-03-15
    Type: Source and taxonomy
  • Version 2.0: 2017-06-28
    Type: Atomic model, Data collection