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The Open Protein Structure Annotation Network
PDB Keyword
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2nyh

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

    Title Crystal structure of putative Dioxygenase (YP_555069.1) from Burkholderia Xenovorans LB400 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 2nyh Target Id 367834
    Related PDB Ids 2p8i 
    Molecular Characteristics
    Source Burkholderia xenovorans lb400
    Alias Ids TPS1926,YP_555069.1, BIG_92, 86345 Molecular Weight 13254.12 Da.
    Residues 116 Isoelectric Point 6.00
    Sequence mtfrdtsaiaswhahvyfdassrdaawtlreqieahwsgklqlgrfherpvgphpmwsyqlaftqeqfa dlvgwltlnhgaldiflhpntgdalrdhrdaavwighshelvlsaln
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.22
    Matthews' coefficent 2.58 Rfactor 0.176
    Waters 363 Solvent Content 52.39

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Burkholderia xenovorans Bxeno_B2751 (Bxe_B0224) gene translates into the amino acid sequence YP_555069 that belongs to the COG family annotated as aromatic ring-cleaving dioxygenases (COG3805) and it is the first member from this large (~100) dihydroxyphenilalanine (DOPA) 4,5-dioxygenase family with a solved structure (PF08883). The functional annotation is based on an experimental study of its Amanita muscaria  homolog [Ref].

     

    An independent model of YP_555069 was solved from a 1.4 A resolution dataset and deposited on the PDB with access code 2p8i. JCSG recently solved another structure from this family, Nostoc punctiforme PCC 73102 protein NPF1925 (2peb).
     

    SCOP classifies 2nyh in the a+b class, ferredoxin-like fold, DOPA-like superfamily, DOPA dioxygenase-like family. Despite the lack of any recognizable sequence similarity to other proteins, 2nyh has a weak hit with DNA-binding domains of the ferredoxin-like fold. For instance, the bovine papillomavirus-1 E2 proteins (PDB: 2bop, 1r8h) [Ref]. Dali Z-score of 6.9 with RMSD 2.4 A on ~60 amino acids; FATCAT p-value of 2.75e-05, RMSD 3.25 A on 80 aa, with only 5% sequence identity. It is difficult to reconcile the sequence and structural similarity based predictions (enzyme - dioxygenase vs. DNA binding). PQS server predicts that 2nyh is a dimeric protein.

    Ligand Summary



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