6J6U

Rat PTPRZ D1-D2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A head-to-toe dimerization has physiological relevance for ligand-induced inactivation of protein tyrosine receptor type Z.

Fujikawa, A.Sugawara, H.Tanga, N.Ishii, K.Kuboyama, K.Uchiyama, S.Suzuki, R.Noda, M.

(2019) J Biol Chem 294: 14953-14965

  • DOI: 10.1074/jbc.RA119.007878
  • Primary Citation of Related Structures:  
    6J6U

  • PubMed Abstract: 
  • Protein-tyrosine phosphatase (PTPase) receptor type Z (PTPRZ) has two receptor isoforms, PTPRZ-A and -B, containing tandem intracellular PTP-D1 and -D2 domains, with only D1 being active. Pleiotrophin (PTN) binding to the extracellular PTPRZ region leads to inactivation of its PTPase activity, thereby facilitating oligodendrocyte precursor cell (OPC) differentiation and myelination in the central nervous system ...

    Protein-tyrosine phosphatase (PTPase) receptor type Z (PTPRZ) has two receptor isoforms, PTPRZ-A and -B, containing tandem intracellular PTP-D1 and -D2 domains, with only D1 being active. Pleiotrophin (PTN) binding to the extracellular PTPRZ region leads to inactivation of its PTPase activity, thereby facilitating oligodendrocyte precursor cell (OPC) differentiation and myelination in the central nervous system. However, the mechanisms responsible for PTN-induced PTPRZ inactivation remain unclear. We herein report that the crystal structure of the intracellular region of PTPRZ (PTPRZ-ICR) shows a "head-to-toe"-type dimer conformation, with D2 masking the catalytic site of D1. MS analyses revealed that PTPRZ-ICR proteins remain in monomer-dimer equilibrium in aqueous solution and that a substrate-derived inhibitory peptide or competitive inhibitor (SCB4380) specifically bind to the monomer form in a 1:1 ratio. A D2 deletion (ΔD2) or dimer interface mutation (DDKK) disrupted dimer formation, but SCB4380 binding was maintained. Similar to WT PTPRZ-B, monomer-biased PTPRZ-B-ΔD2 and PTPRZ-B-DDKK variants efficiently dephosphorylated p190RhoGAP at Tyr-1105 when co-expressed in BHK-21 cells. The catalytic activities of these variants were not suppressed by PTN treatment, but were inhibited by the cell-permeable PTPase inhibitor NAZ2329. Of note, the PTN treatment did not enhance OPC differentiation in primary cultured glial cells from ΔD2 or PTPase-inactive PTPRZ-B (CS) mutant knock-in mice. Our results thus indicate that PTN-induced PTPRZ inactivation results from dimer formation of the intracellular tandem PTP domains in a head-to-toe configuration, which is physiologically relevant to the control of OPC differentiation in vivo .


    Related Citations: 
    • Small-molecule inhibition of PTPRZ suppresses tumor growth in a rat model of glioblastoma.
      Fujikawa, A., Nagahira, A., Sugawara, H., Ishii, K., Imajo, S., Matsumoto, M., Kuboyama, K., Suzuki, R., Tanga, N., Noda, M., Uchiyama, S., Tomoo, T., Ogata, A., Masumura, M., Noda, M.
      (2016) Sci Rep 6:20473: 1
    • Targeting PTPRZ inhibits stem cell-like properties and tumorigenicity in glioblastoma cells.
      Fujikawa, A., Sugawara, H., Tanaka, T., Matsumoto, M., Kuboyama, K., Suzuki, R., Tanga, N., Ogata, A., Masumura, M., Noda, M.
      (2017) Sci Rep 7: 5609

    Organizational Affiliation

    Institute of Innovative Research, Tokyo Institute of Technology, 4529 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase zetaA, B618Rattus norvegicusMutation(s): 0 
Gene Names: Ptprz1PtprzPtpz
EC: 3.1.3.48
UniProt
Find proteins for Q62656 (Rattus norvegicus)
Explore Q62656 
Go to UniProtKB:  Q62656
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.725α = 90
b = 147.585β = 90
c = 65.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-01-15 
  • Released Date: 2019-08-28 
  • Deposition Author(s): Sugawara, H.

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references