4OA7 | pdb_00004oa7

Crystal structure of Tankyrase1 in complex with IWR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.283 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Disruption of Wnt/ beta-Catenin Signaling and Telomeric Shortening Are Inextricable Consequences of Tankyrase Inhibition in Human Cells.

Kulak, O.Chen, H.Holohan, B.Wu, X.He, H.Borek, D.Otwinowski, Z.Yamaguchi, K.Garofalo, L.A.Ma, Z.Wright, W.Chen, C.Shay, J.W.Zhang, X.Lum, L.

(2015) Mol Cell Biol 35: 2425-2435

  • DOI: https://doi.org/10.1128/MCB.00392-15
  • Primary Citation Related Structures: 
    4OA7, 4TOR, 4TOS

  • PubMed Abstract: 

    Maintenance of chromosomal ends (telomeres) directly contributes to cancer cell immortalization. The telomere protection enzymes belonging to the tankyrase (Tnks) subfamily of poly(ADP-ribose) polymerases (PARPs) have recently been shown to also control transcriptional response to secreted Wnt signaling molecules. Whereas Tnks inhibitors are currently being developed as therapeutic agents for targeting Wnt-related cancers and as modulators of Wnt signaling in tissue-engineering agendas, their impact on telomere length maintenance remains unclear. Here, we leveraged a collection of Wnt pathway inhibitors with previously unassigned mechanisms of action to identify novel pharmacophores supporting Tnks inhibition. A multifaceted experimental approach that included structural, biochemical, and cell biological analyses revealed two distinct chemotypes with selectivity for Tnks enzymes. Using these reagents, we revealed that Tnks inhibition rapidly induces DNA damage at telomeres and telomeric shortening upon long-term chemical exposure in cultured cells. On the other hand, inhibitors of the Wnt acyltransferase Porcupine (Porcn) elicited neither effect. Thus, Tnks inhibitors impact telomere length maintenance independently of their affects on Wnt/β-catenin signaling. We discuss the implications of these findings for anticancer and regenerative medicine agendas dependent upon chemical inhibitors of Wnt/β-catenin signaling.


  • Organizational Affiliation
    • Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Macromolecule Content 

  • Total Structure Weight: 100.05 kDa 
  • Atom Count: 7,048 
  • Modeled Residue Count: 819 
  • Deposited Residue Count: 860 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-1
A, B, C, D
215Homo sapiensMutation(s): 0 
Gene Names: TNKSPARP5APARPLTIN1TINF1TNKS1
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95271 (Homo sapiens)
Explore O95271 
Go to UniProtKB:  O95271
PHAROS:  O95271
GTEx:  ENSG00000173273 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95271
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2XS

Query on 2XS



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
4-[(3aR,4R,7S,7aS)-1,3-dioxo-1,3,3a,4,7,7a-hexahydro-2H-4,7-methanoisoindol-2-yl]-N-(quinolin-8-yl)benzamide
C25 H19 N3 O3
ZGSXEXBYLJIOGF-BTYSMDAFSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.283 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.936α = 90
b = 107.936β = 90
c = 121.921γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
CCP4model building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-07
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 1.2: 2015-07-15
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description