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The Open Protein Structure Annotation Network
PDB Keyword
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3bwv

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

    Title Crystal structure of deoxyribonucleotidase-like protein (NP_764060.1) from Staphylococcus epidermidis ATCC 12228 at 1.55 A resolution. To be published
    Site JCSG
    PDB Id 3bwv Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1671,NP_764060.1, 92358
    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 1.87 Rfactor 0.182
    Waters
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    Solvent Content 34.34

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3bwv

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    Protein Summary

    Based on sequence and strucutral homology, JCSG 376319 (Staphylococcus epidermidis atcc 12228) is a putative 5'(3')-deoxyribonucleotidase. It has an identical fold when compared with 1mh9, 1z4k, 2i7d, and 2jau. However, the fold appears to be common amongst many different enzyme families. Like other 5'(3')-deoxyribonucleotidases, 376319 contains a Mg binding site consisting of Asp 9, the backbone oxygen of Asp 11, and Asp 135.



    The 5'(3')-deoxyribonucleotidases have a number of aromatic residues located near the active site which aid in binding the substrate, but these residues are not present in 376319. Part of this region is disordered in 376319, including one Phe, so there may be other possible interactions that are visible in the presence of a suitable binding partner. This suggests that either a different substrate is utilized, or there is an altogether different function.

    This deoxyribonucleotidase-like protein is also similar to histidinol phosphatases and other members of HAD-like SCOP superfamily. The predicted catalytic residues are Asp9 and Asp11. Genomic neighborhood and phylogenetic cooccurrence indicate functional association with choline transport, histidine metabolism and nitric-oxide synthesis.

    Ligand Summary

    Mg is modeled based on crystallization conditions, geometry, and previously solved homologs.

    References

    Reviews

    References

     

    No references found.

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