9EEY

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

• PDB DOI: https://doi.org/10.2210/pdb9EEY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-19 Released: 2024-12-11 
• Deposition Author(s): Guerrero, L., Ebrahim, A., Riley, B.T., Keedy, D.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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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

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 

• PubMed: 39605455 
• 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.

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Organizational Affiliation: 

Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.4 kDa 
• Atom Count: 2,294 
• Modelled Residue Count: 272 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 5	A	305	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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
• Diffraction Data: https://doi.org/10.18430/M39EEY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.673	α = 90
b = 63.621	β = 90
c = 135.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Guerrero, L., Ebrahim, A., Riley, B.T., Keedy, D.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM133769

Revision History  

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