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The Open Protein Structure Annotation Network
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3bl4

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

    Title Crystal structure of uncharacterized protein (YP_829618.1) from Arthrobacter sp. FB24 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3bl4 Target Id 378222
    Molecular Characteristics
    Source Arthrobacter sp. fb24
    Alias Ids TPS1716,YP_829618.1, 92751 Molecular Weight 13020.13 Da.
    Residues 123 Isoelectric Point 5.72
    Sequence msgdsevgteagltlggdgilrltwprgaaitaadaeramlrvnqlcgddrhpmlvdmattadvsrgar avfgrpcqasriallgsspvdrvlanfflginavpcptkfftserdaltwlalt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.20 Rfree 0.248
    Matthews' coefficent 1.99 Rfactor 0.184
    Waters 82 Solvent Content 38.11

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3bl4
    1. The Dehaloperoxidase Paradox
    S Franzen, MK Thompson, RA Ghiladi - et Biophysica Acta (BBA)-Proteins & , 2012 - Elsevier
     

    Protein Summary

    The Arth_0117 gene from Arthrobacter sp. translates into the YP_829618 sequence that does not have a defined Pfam group.

     

    3bl4 structure is a case of domain swapping. The residues 1-74 of one chain and residues 75-123 of another chain form a "monomer".

    3bl4 dimer with domain swapping
    3bl4 monomer formed by residues 1-74 of chain A and rersidues 75-123 of chain B


    Each 3bl4 monomer folds like the two component response regulator (eg. 2che) in that the secondary structural elements are located in similar position, however, the order of the primary sequences vary significantly. 3bl4 obviously does not have response regulator activity since it completely lacks the corresponding active site. Yet, DALI weak but top score (Z=5) is with 3ffw, the chemotactic protein CheY.

    3bl4 is structurally similar (DALI Z-scr=3) to 2 other JCSG structures  2q3l (rmsd 2.7A for 81 aligned CA, 22% seq id) and 2ook (rmsd 2.7A for 88 aligned CA, 22% seq id). Overall, the monomer is more similar to 2ook with the main difference being connecting loop around 74. The helix 63-74 is unique to 3bl4 and it seems to be flexible based on lack of electron density in the crystal. Another observation is that the dimer of 3bl4 is different from 2ook and 2q3l (the dimer of 2q3l can be made similar to 3bl4A although the 3bl4 dimer is likely a crystalization artifact).

    There are very few homologous sequences found in a BLAST (nr) search (YP_829618 sequence is 3rd in the alignment below). It appears that the sequences are very diverse. Only residues 82,110,116,119 are strictly conserved (shown in green in the surface plot below). Other conserved residues include 55,57,61,65,68, 78, 83-90, 92, 94, 98,106, 111, 120 (shown in blue in the surface plot below).

    3bl4 sequence conservation displayed on the dimeric protein surface

    The conserved residues are hydrophobic and form a continuous patch on the protein surface. Thus, it is likely 3bl4 will bind a partner of similar nature, such as peptides or other proteins. It is possible that 3bl4 functions in a signaling pathway like the anti-sigma factor (more work needed in comparison with 1FC6, 1VC1, 1auz, 2F9I, 2D4Q, 1t1d and 2BZR etc). 2q3l and 2ook also have those conserved residues and may have similar functions.
     

    Ligand Summary



    References

    Reviews

    References

     

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