8OEP | pdb_00008oep

Crystal structure of the PTPN3 PDZ domain bound to the HPV18 E6 oncoprotein C-terminal peptide

• PDB DOI: https://doi.org/10.2210/pdb8OEP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, human papillomavirus 18
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-03-11 Released: 2023-05-10 
• Deposition Author(s): Genera, M., Colcombet-Cazenave, B., Croitoru, A., Raynal, B., Mechaly, A., Caillet, J., Haouz, A., Wolff, N., Caillet-Saguy, C.
• Funding Organization(s): Pasteur Institute, Centre National de la Recherche Scientifique (CNRS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Interactions of the protein tyrosine phosphatase PTPN3 with viral and cellular partners through its PDZ domain: insights into structural determinants and phosphatase activity.

Genera, M., Colcombet-Cazenave, B., Croitoru, A., Raynal, B., Mechaly, A., Caillet, J., Haouz, A., Wolff, N., Caillet-Saguy, C.

(2023) Front Mol Biosci 10: 1192621-1192621

• PubMed: 37200868 
• DOI: https://doi.org/10.3389/fmolb.2023.1192621
• Primary Citation Related Structures: 
  8CQY, 8OEP


• PubMed Abstract: 
  

  The human protein tyrosine phosphatase non-receptor type 3 (PTPN3) is a phosphatase containing a PDZ (PSD-95/Dlg/ZO-1) domain that has been found to play both tumor-suppressive and tumor-promoting roles in various cancers, despite limited knowledge of its cellular partners and signaling functions. Notably, the high-risk genital human papillomavirus (HPV) types 16 and 18 and the hepatitis B virus (HBV) target the PDZ domain of PTPN3 through PDZ-binding motifs (PBMs) in their E6 and HBc proteins respectively. This study focuses on the interactions between the PTPN3 PDZ domain (PTPN3-PDZ) and PBMs of viral and cellular protein partners. We solved the X-ray structures of complexes between PTPN3-PDZ and PBMs of E6 of HPV18 and the tumor necrosis factor-alpha converting enzyme (TACE). We provide new insights into key structural determinants of PBM recognition by PTPN3 by screening the selectivity of PTPN3-PDZ recognition of PBMs, and by comparing the PDZome binding profiles of PTPN3-recognized PBMs and the interactome of PTPN3-PDZ. The PDZ domain of PTPN3 was known to auto-inhibit the protein's phosphatase activity. We discovered that the linker connecting the PDZ and phosphatase domains is involved in this inhibition, and that the binding of PBMs does not impact this catalytic regulation. Overall, the study sheds light on the interactions and structural determinants of PTPN3 with its cellular and viral partners, as well as on the inhibitory role of its PDZ domain on its phosphatase activity.

---

Organizational Affiliation: 
• Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France.
Sorbonne Université, Complexité du Vivant, F-75005, Paris, France.
Molecular Biophysics Platform-C2RT, CNRS, Institut Pasteur, Université Paris Cité, Paris, France.
Crystallography Platform-C2RT, Institut Pasteur, Université Paris Cité, Paris, France.
CNRS, Institut de Biologie Physico-Chimique, Université Paris Cité, Paris, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.96 kDa 
• Atom Count: 1,763 
• Modeled Residue Count: 202 
• Deposited Residue Count: 254 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 3	A, C	114	Homo sapiens	Mutation(s): 0  Gene Names: PTPN3, PTPH1 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P26045 (Homo sapiens) Explore P26045  Go to UniProtKB:  P26045
PHAROS:  P26045 GTEx:  ENSG00000070159

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein E6	B, D	13	human papillomavirus 18	Mutation(s): 0
UniProt
Find proteins for P06463 (Human papillomavirus type 18) Explore P06463  Go to UniProtKB:  P06463

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.23	α = 90
b = 82.23	β = 90
c = 139.2	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-10 
Deposition Author(s): Genera, M., Colcombet-Cazenave, B., Croitoru, A., Raynal, B., Mechaly, A., Caillet, J., Haouz, A., Wolff, N., Caillet-Saguy, C.

---

Funding Organization	Location	Grant Number
Pasteur Institute	France	--
Centre National de la Recherche Scientifique (CNRS)	France	--

Revision History  

• Version 1.0: 2023-05-10
  Type: Initial release
  
• Version 1.1: 2023-05-31
  Changes: Database references, Refinement description
• Version 1.2: 2024-06-19
  Changes: Data collection, Refinement description