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1vk6

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

    Title Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 1vk6 Target Id 355840
    Related PDB Ids 2gb5 
    Molecular Characteristics
    Source Escherichia coli k12
    Alias Ids TPS1352,1790429 Molecular Weight 29772.58 Da.
    Residues 257 Isoelectric Point 5.63
    Sequence mdriiekldhgwwvvsheqklwlpkgelpygeranfdlvgqralqigewqgepvwlvqqqrrhdmgsvr qvidldvglfqlagrgvqlaefyrshkycgycghemypsktewamlcshcreryypqiapciivairrd dsillaqhtrhrngvhtvlagfvevgetleqavarevmeesgikvknlryvtsqpwpfpqslmtafmae ydsgdividpkelleanwyryddlpllpppgtvarrliedtvamcraeye
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.20 Rfree 0.21955
    Matthews' coefficent 4.13 Rfactor 0.18668
    Waters 96 Solvent Content 69.99

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vk6
    1. Prediction of active sites for protein structures from computed chemical properties
    J Ko, LF Murga, Y Wei, MJ Ondrechen - Bioinformatics, 2005 - Oxford Univ Press
     
    2. 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
     
    3. Structural and functional diversity of nudix fold
    Y Hua, J Lin, B Tian - Protein and Peptide Letters, 2008 - ingentaconnect.com
     
    4. The first characterised wheat (Triticum aestivum L.) member of the nudix hydrolase family shows specificity for NAD (P)(H) and FAD
    IJ Joye, T Beli_n, JA Delcour - Journal of Cereal Science, 2010 - Elsevier
     
    5. 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
     
    6. Structural and ligand-binding properties of a dual substrate specific enzyme from Schizosaccharomyces pombe
    JA Garza - 2009 - books.google.com
     

    Protein Summary

    The gene 1790429 from Escherichia coli encodes the enzyme NADH pyrophosphatase E.C.3.6.1.22, a member of an NADH pyrophosphatase subfamily of the Nudix hydrolases PF00293.  The enzyme catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP.  Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity.  The amino acid motif getleqavarevmeesgis highly conserved among family members and functions as a metal binding and catalytic site.   The E.coli enzyme contains three cleary defined structural domains with specific functions:  a rudimentary NUDIX-like domain PF09296, a NADH pyrophosphatase zinc ribbon domain PF09297, and NUDIX domain. It appears to be the first structure  available with such a quaternary arrangement of these domains.  The structure of this enzyme has  also been solved in a different crystal form 2GB5.  The two structures present a similar dimeric architecture (for 1vk6 the second subunit is generated by crystallographic symmetry). All three domains contribute to the dimerization interface.

    Ligand Summary


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