6L03

structure of PTP-MEG2 and MUNC18-1-pY145 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

PTP-MEG2 regulates quantal size and fusion pore opening through two distinct structural bases and substrates.

Xu, Y.F.Chen, X.Yang, Z.Xiao, P.Liu, C.H.Li, K.S.Yang, X.Z.Wang, Y.J.Zhu, Z.L.Xu, Z.G.Zhang, S.Wang, C.Song, Y.C.Zhao, W.D.Wang, C.H.Ji, Z.L.Zhang, Z.Y.Cui, M.Sun, J.P.Yu, X.

(2021) EMBO Rep 22: e52141-e52141

  • DOI: https://doi.org/10.15252/embr.202052141
  • Primary Citation of Related Structures:  
    6KZQ, 6L03

  • PubMed Abstract: 

    Tyrosine phosphorylation of secretion machinery proteins is a crucial regulatory mechanism for exocytosis. However, the participation of protein tyrosine phosphatases (PTPs) in different exocytosis stages has not been defined. Here we demonstrate that PTP-MEG2 controls multiple steps of catecholamine secretion. Biochemical and crystallographic analyses reveal key residues that govern the interaction between PTP-MEG2 and its substrate, a peptide containing the phosphorylated NSF-pY 83 site, specify PTP-MEG2 substrate selectivity, and modulate the fusion of catecholamine-containing vesicles. Unexpectedly, delineation of PTP-MEG2 mutants along with the NSF binding interface reveals that PTP-MEG2 controls the fusion pore opening through NSF independent mechanisms. Utilizing bioinformatics search and biochemical and electrochemical screening approaches, we uncover that PTP-MEG2 regulates the opening and extension of the fusion pore by dephosphorylating the DYNAMIN2-pY 125 and MUNC18-1-pY 145 sites. Further structural and biochemical analyses confirmed the interaction of PTP-MEG2 with MUNC18-1-pY 145 or DYNAMIN2-pY 125 through a distinct structural basis compared with that of the NSF-pY 83 site. Our studies thus provide mechanistic insights in complex exocytosis processes.


  • Organizational Affiliation

    Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 9307Homo sapiensMutation(s): 0 
Gene Names: PTPN9
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P43378 (Homo sapiens)
Explore P43378 
Go to UniProtKB:  P43378
PHAROS:  P43378
GTEx:  ENSG00000169410 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43378
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
stxbp1-pY145 peptideB [auth F]9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61764 (Homo sapiens)
Explore P61764 
Go to UniProtKB:  P61764
PHAROS:  P61764
GTEx:  ENSG00000136854 
Entity Groups  
UniProt GroupP61764
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
B [auth F]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.048α = 90
b = 84.074β = 90
c = 48.753γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary