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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
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    Related PDB Ids 1vk6 
    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1917,1790429
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

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

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    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
     

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    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

    References

     

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