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The Open Protein Structure Annotation Network
PDB Keyword
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2qmq

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of the human N-Myc downstream-regulated gene 2 protein provides insight into its role as a tumor suppressor. J.Biol.Chem. 286 12450-12460 2011
    Site JCSG
    PDB Id 2qmq Target Id 358981
    Molecular Characteristics
    Source Mus musculus
    Alias Ids TPS1410,15277975 Molecular Weight 30520.12 Da.
    Residues 274 Isoelectric Point 5.21
    Sequence thsvetpygsvtftvygtpkpkrpaiftyhdvglnykscfqplfrfgdmqeiiqnfvrvhvdapgmeeg apvfplgyqypsldqladmipcilqylnfstiigvgvgagayilsryalnhpdtveglvlinidpnakg wmdwaahkltgltssipdmilghlfsqeelsgnseliqkyrgiiqhapnlenielywnsynnrrdlnfe rggettlkcpvmlvvgdqaphedavvecnskldptqtsflkmadsggqpqltqpgklteafkyflqg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.183
    Matthews' coefficent 2.08 Rfactor 0.145
    Waters 314 Solvent Content 40.93

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2qmq
    1. NDRG2: a Myc-repressed gene involved in cancer and cell stress
    L Yao, J Zhang, X Liu - Acta biochimica et biophysica Sinica, 2008 - abbs.oxfordjournals.org
     
    2. Crystal Structure of the Human N-Myc Downstream-regulated Gene 2 Protein Provides Insight into Its Role as a Tumor Suppressor
    J Hwang, Y Kim, HB Kang, L Jaroszewski - Journal of Biological , 2011 - ASBMB
     
    3. BMB| CR
    AB Lorentzena, C Mitchelmorea - 2012 - forskning.ruc.dk
     
    4. The unusual extended C-terminal helix of the peroxisomal [alpha]/[beta]-hydrolase Lpx1 is involved in dimer contacts but dispensable for dimerization
    S Thoms, J Hofhuis, C Thing, J Grtner - Journal of structural , 2011 - Elsevier
     

    Protein Summary

    The gene Ndrg2 from Mus musculus encodes for the N-myc downstream regulated 2 (NDRG2) protein (NP_001139431) with 357 residues and characterized by the presence of an esterase/lipase motif from positions 26 to 304. NDRG2 belongs to the family PF03096.  The expression of NDRG2 is repressed by the proto-oncogenes N-myc and c-myc.  

    The 26-299 protein fragment was solved and its structure (2qmq) belongs to the class of alpha and beta proteins (a+b), and reveals an alpha/beta hydrolase fold, specifically in the family of carbon-carbon bond hydrolases SCOP53522. A search for structurally similar proteins using 2qmq as query returns as top hits the sigma factor regulation protein RSBQ 1wom (Z=25), the chloroperoxidase-L 1a88, a bromoperoxidase 3fob, and an arylesterase 3hi4 (Z=24).

    The association with a hydrolase family might suggest that NDRG2 might possess enzymatic function.  For instance, 2qmq structure is highly similar to that of 2-hydroxyl-6-oxo-6-phenylhexa-2,4-dienoic Acid (Hpda) hydrolase (Bphd Enzyme) from Rhodococcus Sp. PDB:1c4x (Z=23).  The microbial Bphd enzyme is involved in the degradation of aromatic compounds, and is  a potent polychlorinated biphenyls (PCBs) degrader.  However, in the context of a mammalian cell, this protein might be another curious case of adaptation of an enzymatic fold type to a signal transduction role.  See entry 2FMU, for example.  In this case, the protein requires binding of an aromatic substrate (e.g. steroid hormone) to fulfill the regulatory function.  Curiously, NDRG2 gene is found to be fused to ERG gene (coding ERG transcription factor) in hormone sensitive prostate cancer [Ref].  The fusion is predicted to code for a chimeric protein.  Within the fusion with the ERG transcription factor, NDRG2 most probably has a regulatory role, enhancing transcription in the presence of steroid hormones.

    Ligand Summary



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