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The Open Protein Structure Annotation Network
PDB Keyword
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3dkq

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

    Title Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at 2.26 A resolution. To be published
    Site JCSG
    PDB Id 3dkq Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS9378,YP_001051978.1, BIG_210, 88640
    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 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.98 Rfactor 0.196
    Waters
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    Solvent Content 58.66

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3dkq
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

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    Protein Summary

    The Sbal_3634 gene from Shewanella baltica os155 encodes a prolyl hydroxylase (PF03171, COG3128) that adopts a jelly-roll fold typical of 2-oxoglytarate dioxygenases and shows signicant similarity to other prolyl hydroxylases, including hypoxia-inducible factor (HIF) prolyl-4 hydroxylase from humans (PDB id: 2HBT, FATCAT P-value 3.81e-06, rmsd 3.06 Å over 150 residues with 10.7% sequence identity) and algae (PDB id: 2JIJ, FATCAT P-value 1.09e-05, rmsd 3.05 over 144 residues with 10.3% identity). HIF prolyl hydroxylases are implicated in collagen synthesis and oxygen homeostasis and their active site, that accomodates proline-rich peptides, exhibits large structural plasticity [Ref]

     

    Zn2+ and pyridine 2,4-dicarboxylate are competitive inhibitors of this enzyme, with respect to Fe2+ and 2-oxoglutarate [Ref], so it would be interesting to see if this is the case too in Sbal_3634 (i.e. if nickel and imidazole ligands observed in structure occupy similar positions).

    Ligand Summary

    Reviews

    References

     

    1. (No Results)

       


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