2QMQ

Crystal structure of a n-myc downstream regulated 2 protein (ndrg2, syld, ndr2, ai182517, au040374) from mus musculus at 1.70 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the human N-Myc downstream-regulated gene 2 protein provides insight into its role as a tumor suppressor.

Hwang, J.Kim, Y.Kang, H.B.Jaroszewski, L.Deacon, A.M.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: 12450-12460

  • DOI: 10.1074/jbc.M110.170803
  • Primary Citation of Related Structures:  

  • 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 ma ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein NDRG2
A
286Mus musculusMutation(s): 0 
Gene Names: Ndrg2 (Kiaa1248, Ndr2)
Find proteins for Q9QYG0 (Mus musculus)
Go to UniProtKB:  Q9QYG0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
2PE
Query on 2PE

Download SDF File 
Download CCD File 
A
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 46.371α = 90.00
b = 46.371β = 90.00
c = 214.749γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
MolProbitymodel building
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence, Refinement description