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2gb5

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

    Title Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 2gb5 Target Id 355840
    Related PDB Ids 1vk6 
    Molecular Characteristics
    Source Escherichia coli k12
    Alias Ids TPS1917,1790429 Molecular Weight 29772.58 Da.
    Residues 257 Isoelectric Point 5.63
    Sequence mdriiekldhgwwvvsheqklwlpkgelpygeranfdlvgqralqigewqgepvwlvqqqrrhdmgsvr qvidldvglfqlagrgvqlaefyrshkycgycghemypsktewamlcshcreryypqiapciivairrd dsillaqhtrhrngvhtvlagfvevgetleqavarevmeesgikvknlryvtsqpwpfpqslmtafmae ydsgdividpkelleanwyryddlpllpppgtvarrliedtvamcraeye
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.30 Rfree 0.252
    Matthews' coefficent 2.36 Rfactor 0.198
    Waters 240 Solvent Content 47.44

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2gb5
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. PIEEfficient filters and coarse grained potentials for unbound proteinprotein docking
    DVS Ravikant, R Elber - Proteins: Structure, Function, and , 2010 - Wiley Online Library
     
    3. Mutational analysis of the AtNUDT7 Nudix hydrolase from Arabidopsis thaliana reveals residues required for protein quarternary structure formation and activity
    K Olejnik, D Plochocka, M Grynberg, G Goch - Acta Biochimica , 2009 - actabp.pl
     
    4. Comparative analysis of mycobacterial NADH pyrophosphatase isoforms reveals a novel mechanism for isoniazid and ethionamide inactivation
    XD Wang, J Gu, T Wang, LJ Bi, ZP Zhang - Molecular , 2011 - Wiley Online Library
     

    Protein Summary

    This structure (SCOP) contains two Nudix domains and a zinc ribbon motif.  One of the nudix domain lost the catalytic site.

    Nudix (or "MutT") hydrolase family enzymes hydrolyze a nucleoside diphosphate linked to some other moiety, X.
    They can be divided into three subfamilies: ADPRase (ADP-ribose pyrophosphatases),ApnAase (Adenosine-(p)n-Adenosine hydrolases) and NADHase (NADH pyrophosphatases). The Nudix enzymes have a signiture sequence GX5EX7REUXEEXGU, U=I/L/V. They generally need di-covalent metals for activity and function as dimers. Their functional roles in cell to as house keepers to sanitize the cell.

    NADHase belongs to NUDC subfamily which catalyze reaction:

    NADH => NMNH+AMP  (Mg2+ needed)

    It predominately favors NADH over NAD+ (120 fold), also has activity for NADPH, ADP-ribose, FAD etc; 2nd nucleotide seems essential for optimal activity. It was also characterized in S. cerevisiae, C. elegans and homo sapiens


    Ligand Summary





    References

    Reviews

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