The Open Protein Structure Annotation Network
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    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 376319
    Molecular Characteristics
    Source Staphylococcus epidermidis atcc 12228
    Alias Ids TPS1671,NP_764060.1, 92358 Molecular Weight 20992.04 Da.
    Residues 179 Isoelectric Point 5.46
    Sequence mtrqriaidmdevladtlgavvkavneradlnikmeslngkklkhmipeheglvmdilkepgffrnldv mphaqevvkqlnehydiyiataamdvptsfhdkyewlleyfpfldpqhfvfcgrkniiladyliddnpk qleifegksimftashnvyehrfervsgwrdvknyfnsiek
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.55 Rfree 0.223
    Matthews' coefficent 1.87 Rfactor 0.182
    Waters 181 Solvent Content 34.34

    Ligand Information


    Google Scholar output for 3bwv

    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.





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