4IKC

Crystal Structure of catalytic domain of PTPRQ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the dephosphorylating activity of PTPRQ towards phosphatidylinositide substrates

Yu, K.R.Kim, Y.J.Jung, S.K.Ku, B.Park, H.Cho, S.Y.Jung, H.Chung, S.J.Bae, K.H.Lee, S.C.Kim, B.Y.Erikson, R.L.Ryu, S.E.Kim, S.J.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1522-1529

  • DOI: https://doi.org/10.1107/S0907444913010457
  • Primary Citation of Related Structures:  
    4IKC

  • PubMed Abstract: 

    Unlike other classical protein tyrosine phosphatases (PTPs), PTPRQ (PTP receptor type Q) has dephosphorylating activity towards phosphatidylinositide (PI) substrates. Here, the structure of the catalytic domain of PTPRQ was solved at 1.56 Å resolution. Overall, PTPRQ adopts a tertiary fold typical of other classical PTPs. However, the disordered M6 loop of PTPRQ surrounding the catalytic core and the concomitant absence of interactions of this loop with residues in the PTP loop results in a flat active-site pocket. On the basis of structural and biochemical analyses, it is proposed that this structural feature might facilitate the accommodation of large substrates, making it suitable for the dephosphorylation of PI substrates. Moreover, subsequent kinetic experiments showed that PTPRQ has a strong preferences for PI(3,4,5)P3 over other PI substrates, suggesting that its regulation of cell survival and proliferation reflects downregulation of Akt signalling.


  • Organizational Affiliation

    Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphotidylinositol phosphatase PTPRQ281Homo sapiensMutation(s): 1 
Gene Names: PTPRQ
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMZ3 (Homo sapiens)
Explore Q9UMZ3 
Go to UniProtKB:  Q9UMZ3
PHAROS:  Q9UMZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UMZ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.58α = 90
b = 77.58β = 90
c = 85.24γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description