2XMR

Crystal structure of human NDRG2 protein provides insight into its role as a tumor suppressor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Human Ndrg2 Protein Provides Insight Into its Role as a Tumor Suppressor.

Hwang, J.Kim, Y.Kang, H.B.Jaroszewski, L.Deacon, A.Lee, H.Choi, W.C.Kim, K.J.Kim, C.H.Kang, B.S.Lee, J.O.Oh, T.K.Kim, J.W.Wilson, I.A.Kim, M.H.

(2011) J Biol Chem 286: 12450

  • DOI: https://doi.org/10.1074/jbc.M110.170803
  • Primary Citation of Related Structures:  
    2QMQ, 2XMQ, 2XMR, 2XMS

  • PubMed Abstract: 

    Considerable attention has recently been paid to the N-Myc downstream-regulated gene (NDRG) family because of its potential as a tumor suppressor in many human cancers. Primary amino acid sequence information suggests that the NDRG family proteins may belong to the α/β-hydrolase (ABH) superfamily; however, their functional role has not yet been determined. Here, we present the crystal structures of the human and mouse NDRG2 proteins determined at 2.0 and 1.7 Å resolution, respectively. Both NDRG2 proteins show remarkable structural similarity to the ABH superfamily, despite limited sequence similarity. Structural analysis suggests that NDRG2 is a nonenzymatic member of the ABH superfamily, because it lacks the catalytic signature residues and has an occluded substrate-binding site. Several conserved structural features suggest NDRG may be involved in molecular interactions. Mutagenesis data based on the structural analysis support a crucial role for helix α6 in the suppression of TCF/β-catenin signaling in the tumorigenesis of human colorectal cancer, via a molecular interaction.


  • Organizational Affiliation

    Division of Biosystems Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN NDRG2
A, B, C
281Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UN36 (Homo sapiens)
Explore Q9UN36 
Go to UniProtKB:  Q9UN36
GTEx:  ENSG00000165795 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UN36
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.232α = 90
b = 88.049β = 90
c = 126.907γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Database references, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description