9EEY

STEP (PTPN5) with active-site disulfide bond and allosteric-site loop shift


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Three STEPs forward: A trio of unexpected structures of PTPN5.

Guerrero, L.Ebrahim, A.Riley, B.T.Kim, S.H.Bishop, A.C.Wu, J.Han, Y.N.Tautz, L.Keedy, D.A.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.11.20.624168
  • Primary Citation of Related Structures:  
    9EEX, 9EEY, 9EEZ

  • PubMed Abstract: 

    Protein tyrosine phosphatases (PTPs) play pivotal roles in myriad cellular processes by counteracting protein tyrosine kinases. Striatal-enriched protein tyrosine phosphatase (STEP, PTPN5) regulates synaptic function and neuronal plasticity in the brain and is a therapeutic target for several neurological disorders. Here, we present three new crystal structures of STEP, each with unexpected features. These include high-resolution conformational heterogeneity at multiple sites, a highly coordinated citrate molecule that inhibits enzyme activity, a previously unseen conformational change at an allosteric site, an intramolecular disulfide bond that was characterized biochemically but had never been visualized structurally, and two serendipitous covalent ligand binding events at surface-exposed cysteines that are nearly or entirely unique to STEP among human PTPs. Together, our results offer new views of the conformational landscape of STEP that may inform structure-based design of allosteric small molecules to specifically inhibit this biomedically important enzyme.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 5305Homo sapiensMutation(s): 0 
Gene Names: PTPN5
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P54829 (Homo sapiens)
Explore P54829 
Go to UniProtKB:  P54829
PHAROS:  P54829
GTEx:  ENSG00000110786 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54829
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.673α = 90
b = 63.621β = 90
c = 135.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133769

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release