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The Open Protein Structure Annotation Network
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3ef8

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

    Title Crystal structure of Putative Scyalone Dehydratase (YP_496742.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3ef8 Target Id 367578
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS6325,YP_496742.1, 3.10.450.50, 86370 Molecular Weight 17209.51 Da.
    Residues 149 Isoelectric Point 5.86
    Sequence mtdtnlvemraiermmfdysyhldmnhpeelaalfvedcevsyapnfgatgrdaykktlegigtffrgt shhnsnicidfvseteanvrsvvlaihrytkerpdgilygqyfdtvvkvdgqwkfkrrelrttmttdyh vraanpigrae
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.50 Rfree 0.188
    Matthews' coefficent 2.33 Rfactor 0.163
    Waters 234 Solvent Content 47.19

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    YP_496742.1 is from Novosphingobium aromaticivorans.  Exposure to N. aromaticivorans may tigger the develop of primary biliary cirrhosis (see reference #1).  This protein is a member of the Ring_hydroxyl_B (PF00866) family from Pfam which is part of the NTF2_like Super-family (cl09109) from the Conserved Domain Database. Structurally, it is similar to scytalone dehydratase(PDB code: 3STD), Ca2+/calmodulin-dependent kinase (PDB code: 1HKX), nuclear transport factor 2 (NTF2, PDB code: 1A2K) and a Ntf2-like protein of unknown function (PDB code: 3B8L), which also has a TOPSAN page.  Most of the residues in the active site of scyalone dehydratase seem to be conserved.  In figure 2 (see below), Tyr50, His85, His110, and Asn131 from scyalone dehydratase can be aligned to Tyr43, His71, His103, and Tyr111, respectively, from the protein encoded by YP_496741.1, which suggests that this protein might be a scyalone dehydratase.  However, Tyr30 from scyalone dehydratase aligns to Leu23 from this protein.  Crystallographic packing analysis suggests that the biological form of this molecule is a trimer.



    Figure 1: A structural superimposition of the protein encoded by YP_496741.1 shown in magneta superimposed with scytalone dehydratase(PDB code: 3STD) shown in blue.  RMSD 2.0, sequence identity 14.3%, and 133 residues aligned.


    Figure 2: A structural superimposition of the protein encoded by YP_496741.1 shown in magneta superimposed with scytalone dehydratase(PDB code: 3STD) shown in blue.  Conserved active site residues are highlighted in yellow (Tyr50, His85, His110, and Asn131 from scyalone dehydratase can be aligned to Tyr43, His71, His103, and Tyr111, respectively, from the protein encoded by YP_496741.1).  Tyr30 from the active site of scyalone dehydratase aligns to Leu23 from this protein is highlighted in green.



     



























    Ligand Summary

    PEG

    Reviews

    References

     

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