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: 1.70 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NDRG2A286Mus musculusMutation(s): 0 
Gene Names: 15277975Ndrg2Kiaa1248Ndr2
UniProt
Find proteins for Q9QYG0 (Mus musculus)
Explore Q9QYG0 
Go to UniProtKB:  Q9QYG0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
E [auth A]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
BEZ
Query on BEZ

Download Ideal Coordinates CCD File 
D [auth A]BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.371α = 90
b = 46.371β = 90
c = 214.749γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description