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The Open Protein Structure Annotation Network
PDB Keyword
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3nl9

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

    Title Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15. Acta Crystallogr.,Sect.F 66 1237-1244 2010
    Site JCSG
    PDB Id 3nl9 Target Id 378014
    Molecular Characteristics
    Source Exiguobacterium sibiricum 255-15
    Alias Ids TPS1705,YP_001813558.1, 92168 Molecular Weight 19083.68 Da.
    Residues 170 Isoelectric Point 4.93
    Sequence mkqpnyyqdvkqfhqtfhhpgadqptaipldrgvkratwtaeeavveflhqssqneteflaaietfkag ldqavkkslketypvteverlvgqgdaltdalyfimgsfveaglepgplfeivqqanmaklgpdgqpif resdqkvmkpdgwlppepqleaevvrqmkeka
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.78 Rfree 0.222
    Matthews' coefficent 2.16 Rfactor 0.177
    Waters 141 Solvent Content 43.07

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nl9
    1. Structure of a putative NTP pyrophosphohydrolase: YP_001813558. 1 from Exiguobacterium sibiricum 255-15
    GW Han, MA Elsliger, TO Yeates, Q Xu - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    This protein is a putative NTP Pyrophosphohydrolase and is related to 1vmg (structure determined at the JCSG) and 1w2y. This protein displays an interesting segment-swapping (not previously observed for this family) and the putative metal-binding site (by similarity to 1vmg and 1w2y) is formed only upon dimerization and segment swapping. The metal binding residues in MazG (PDB: 1vmg) are Glu 35, Glu 38, Glu 54 and Asp 57. In dUTPase (PDB: 1w2y) which is related by an ancestral duplication to 1vmg the metal binding residues are Glu 46, Glu 49, Glu 74 and Asp 77 although the C-terminal MazG-like domain has lost its ability to bind metal. In this structure, there are two metal binding sites (related by symmetry) and the biological active protein can only be formed upon dimerization. The first metal-binding site is formed by residues Glu 43 and Glu 47  of the polypeptide (chain A) while the remaining residues of the metal binding site are comprised of residues Asp 95 and Asp 99 of a symmetry-related molecule. Similarly, the other (symmetry-related) metal binding site is formed by residues Asp 95 and Asp 99 of the main polypeptide (chain A) and the rest of the metal-binding site contributed by Glu 43 and Glu 47 of the symmetry related molecule. Although no biologically relevant ligand is seen in our structure, a glycerol molecule is present at a position similar to the DUN site in dUTPase (PDB: 1w2y).

    Ligand Summary

    No biologically relevant ligand at the active site although a glycerol molecule is present in the putative nucleotide binding site.

    Putative metal binding residues are Glu 43, Glu 47, Asp 95 (chain A) and Asp 99 (chain B; a symmetry-related molecule).

    References

    Reviews

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