5GTJ | pdb_00005gtj

CRYSTAL STRUCTURE OF CATALYTICALLY ACTIVE FORM OF HUMAN DUSP26


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5GTJ

This is version 1.1 of the entry. See complete history

Literature

Structural Insight into the Critical Role of the N-Terminal Region in the Catalytic Activity of Dual-Specificity Phosphatase 26

Won, E.Y.Lee, S.O.Lee, D.H.Lee, D.Bae, K.H.Lee, S.C.Kim, S.J.Chi, S.W.

(2016) PLoS One 11: e0162115-e0162115

  • DOI: https://doi.org/10.1371/journal.pone.0162115
  • Primary Citation Related Structures: 
    5GTJ

  • PubMed Abstract: 

    Human dual-specificity phosphatase 26 (DUSP26) is a novel target for anticancer therapy because its dephosphorylation of the p53 tumor suppressor regulates the apoptosis of cancer cells. DUSP26 inhibition results in neuroblastoma cell cytotoxicity through p53-mediated apoptosis. Despite the previous structural studies of DUSP26 catalytic domain (residues 61-211, DUSP26-C), the high-resolution structure of its catalytically active form has not been resolved. In this study, we determined the crystal structure of a catalytically active form of DUSP26 (residues 39-211, DUSP26-N) with an additional N-terminal region at 2.0 Å resolution. Unlike the C-terminal domain-swapped dimeric structure of DUSP26-C, the DUSP26-N (C152S) monomer adopts a fold-back conformation of the C-terminal α8-helix and has an additional α1-helix in the N-terminal region. Consistent with the canonically active conformation of its protein tyrosine phosphate-binding loop (PTP loop) observed in the structure, the phosphatase assay results demonstrated that DUSP26-N has significantly higher catalytic activity than DUSP26-C. Furthermore, size exclusion chromatography-multiangle laser scattering (SEC-MALS) measurements showed that DUSP26-N (C152S) exists as a monomer in solution. Notably, the crystal structure of DUSP26-N (C152S) revealed that the N-terminal region of DUSP26-N (C152S) serves a scaffolding role by positioning the surrounding α7-α8 loop for interaction with the PTP-loop through formation of an extensive hydrogen bond network, which seems to be critical in making the PTP-loop conformation competent for phosphatase activity. Our study provides the first high-resolution structure of a catalytically active form of DUSP26, which will contribute to the structure-based rational design of novel DUSP26-targeting anticancer therapeutics.


  • Organizational Affiliation
    • Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 83.12 kDa 
  • Atom Count: 5,849 
  • Modeled Residue Count: 668 
  • Deposited Residue Count: 724 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual specificity protein phosphatase 26
A, B, C, D
181Homo sapiensMutation(s): 1 
Gene Names: DUSP26DUSP24LDP4MKP8NATA1SKRP3
EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BV47 (Homo sapiens)
Explore Q9BV47 
Go to UniProtKB:  Q9BV47
PHAROS:  Q9BV47
GTEx:  ENSG00000133878 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BV47
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.617α = 90
b = 100.803β = 114.67
c = 70.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary