3RGO

Crystal Structure of PTPMT1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.928 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural and functional analysis of PTPMT1, a phosphatase required for cardiolipin synthesis.

Xiao, J.Engel, J.L.Zhang, J.Chen, M.J.Manning, G.Dixon, J.E.

(2011) Proc.Natl.Acad.Sci.USA 108: 11860-11865

  • DOI: 10.1073/pnas.1109290108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PTPMT1 (PTP localized to the Mitochondrion 1) is a member of the protein tyrosine phosphatase superfamily that is localized exclusively to the mitochondrion. We recently reported that PTPMT1 dephosphorylates phosphatidylglycerol phosphate, an essenti ...

    PTPMT1 (PTP localized to the Mitochondrion 1) is a member of the protein tyrosine phosphatase superfamily that is localized exclusively to the mitochondrion. We recently reported that PTPMT1 dephosphorylates phosphatidylglycerol phosphate, an essential intermediate of cardiolipin biosynthesis. To gain further insights into the molecular basis of PTPMT1 function, we determined the crystal structures of the phosphatase domain of PTPMT1. PTPMT1 exhibits a canonical protein tyrosine phosphatase domain fold, resembling many dual-specificity phosphatases such as phosphatase and tensin homolog and vaccinia H1-related phosphatase. We also determined the structure of the catalytically inactive phosphatase in complex with a surrogate substrate, phosphatidylinositol 5-phosphate, which sheds light on the substrate recognition and specificity of PTPMT1. Comparison of the apo and substrate-bound structures of PTPMT1 suggests that it undergoes significant conformational change during catalysis, and we further demonstrated that an evolutionarily conserved EEYE loop is important for its activity.


    Organizational Affiliation

    Department of Pharmacology, University of California, La Jolla, CA 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-tyrosine phosphatase mitochondrial 1
A
157Mus musculusMutation(s): 0 
Gene Names: Ptpmt1 (Plip)
EC: 3.1.3.27
Find proteins for Q66GT5 (Mus musculus)
Go to UniProtKB:  Q66GT5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.928 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.227 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 36.453α = 90.00
b = 36.453β = 90.00
c = 230.024γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-04-08 
  • Released Date: 2011-07-06 
  • Deposition Author(s): Xiao, J., Engel, J.L.

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-20
    Type: Database references
  • Version 1.3: 2011-08-03
    Type: Database references
  • Version 1.4: 2017-11-08
    Type: Refinement description