6UZT | pdb_00006uzt

Crystal Structure of RPTP alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.191 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6UZT

This is version 1.2 of the entry. See complete history

Literature

RPTP alpha phosphatase activity is allosterically regulated by the membrane-distal catalytic domain.

Wen, Y.Yang, S.Wakabayashi, K.Svensson, M.N.D.Stanford, S.M.Santelli, E.Bottini, N.

(2020) J Biological Chem 295: 4923-4936

  • DOI: https://doi.org/10.1074/jbc.RA119.011808
  • Primary Citation Related Structures: 
    6UZT

  • PubMed Abstract: 

    Receptor-type protein tyrosine phosphatase α (RPTPα) is an important positive regulator of SRC kinase activation and a known promoter of cancer growth, fibrosis, and arthritis. The domain structure of RPTPs comprises an extracellular region, a transmembrane helix, and two tandem intracellular catalytic domains referred to as D1 and D2. The D2 domain of RPTPs is believed to mostly play a regulatory function; however, no regulatory model has been established for RPTPα-D2 or other RPTP-D2 domains. Here, we solved the 1.8 Å resolution crystal structure of the cytoplasmic region of RPTPα, encompassing D1 and D2, trapped in a conformation that revealed a possible mechanism through which D2 can allosterically inhibit D1 activity. Using a D2-truncation RPTPα variant and mutational analysis of the D1/D2 interfaces, we show that D2 inhibits RPTPα phosphatase activity and identified a 405 PFTP 408 motif in D1 that mediates the inhibitory effect of D2. Expression of the gain-of-function F406A/T407A RPTPα variant in HEK293T cells enhanced SRC activation, supporting the relevance of our proposed D2-mediated regulation mechanism in cell signaling. There is emerging interest in the development of allosteric inhibitors of RPTPs but a scarcity of validated allosteric sites for RPTPs. The results of our study not only shed light on the regulatory role of RPTP-D2 domains, but also provide a potentially useful tool for the discovery of chemical probes targeting RPTPα and other RPTPs.


  • Organizational Affiliation
    • Department of Medicine, University of California, San Diego, La Jolla, California 92037.

Macromolecule Content 

  • Total Structure Weight: 139.22 kDa 
  • Atom Count: 11,211 
  • Modeled Residue Count: 1,159 
  • Deposited Residue Count: 1,202 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase alpha
A, B
601Homo sapiensMutation(s): 0 
Gene Names: PTPRAPTPAPTPRL2
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18433 (Homo sapiens)
Explore P18433 
Go to UniProtKB:  P18433
PHAROS:  P18433
GTEx:  ENSG00000132670 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18433
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.72α = 90
b = 112.11β = 90
c = 136.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesAR066053

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description