The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of NTF2-like protein of unknown function (YP_001165924.1) from Novosphingobium aromaticivorans DSM 12444 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 3b8l Target Id 378138
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS1710,YP_001165924.1, 3.10.450.50, 103295 Molecular Weight 15934.24 Da.
    Residues 144 Isoelectric Point 5.20
    Sequence mqcpiedrlaiqdlmiayahavdtvsdidavldvftedavfdlsgigltpqvghagirefftnvfanms hhahyltnfavtgyegdtasmrayvigmgvgkdgravtvngryffevrrtekgwkatrytmdflmplsg tldnak
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 1.75 Rfree 0.199
    Matthews' coefficent 2.39 Rfactor 0.167
    Waters 968 Solvent Content 48.43

    Ligand Information


    Google Scholar output for 3b8l
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org

    Protein Summary

    The Saro_3538 gene from Novosphingobium aromaticivorans dsm 12444 encodes a homolog of the SnoaL-like polyketide cyclase family (PF07366), member of the NTF2-like superfamily. PISA predicts that the protein associates into a trimer. Although the function of Saro_3538 is unknown, genome context suggests an association with the ETDE (ethyl tert-butyl ether degradation) system. This in turn may suggest a function as an aromatic ring hydroxylase (PF00866, another member of the NTF2-like superfamily) implicated in the degradation of aromatic chain hydrocarbons present for example in petroleum products (e.g. benzene, toluene, xylene). The Sphingomonas species is noted for its ability to degrade a wide range of such hydrocarbons [Ref].


    Despite low sequence identity (7% after structural alignment) the structure resembles the beta (small, non catalytic) subunit of PAH dioxygenase from sphingomonas SP CHY-1 [Ref] (pdb code 2ckf) in both tertiary fold (P-value 5.34e-09 when aligned with rigid fatcat) and quaternary arrangement of the subunits. Other examples of similar trimeric structures in the pdb are the beta subunit of benzoate 1,2-dioxygenase from Burkholderia Mallei  (pdb 3e99, 15% identity), a putative scytalone dehydratase (pdb 3ef8, 16%) and the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (pdb 3eby, 14%), both from the same organism.


    To do: compare with even more ring hydroxylases found in the same organism - see [Ref]. Look for corresponding alpha subunit, or for structural evidence of an active site.


    NTF2-like protein of unknown function. NTF2-like family contains: NTF2, scytalone dehydratase, ketosteroid isomerases, and a domain of CaMKII.

    Ligand Summary





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