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The Open Protein Structure Annotation Network
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3fjv

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

    Title Crystal structure of novel protein of unknown function (YP_111841.1) from BURKHOLDERIA PSEUDOMALLEI K96243 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3fjv Target Id 381695
    Molecular Characteristics
    Source Burkholderia pseudomallei k96243
    Alias Ids TPS24758,YP_111841.1, BIG_450, 104797 Molecular Weight 21766.45 Da.
    Residues 193 Isoelectric Point 5.28
    Sequence mtltrdslltleayakvrrqeharviahkkrravsignhlrllfedettiryqihemlhiekifdedgi qaeldaylplvpdgsnlkatlqieyenetqrraalarlvgiedrvflrvddeapvyaiadedlerdtae ktsavhflrfelgdamkaklkagaplsigcdhphypiqaaridpdvaaslagdld
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.219
    Matthews' coefficent 2.44 Rfactor 0.181
    Waters 345 Solvent Content 49.50

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    YP_111841.1 encodes a novel protein of unknown function. It contains two domains, domain I (1:31, 46:81) is a helical domain, domain II (32:45,82-193) is a mainly beta protein with a beta barrel. YP_111841.1 likely functions as a dimer according to crystal contacts. Sequence search didn't identify a homolog with known function. The gene neighbourhood analysis suggests that this protein is likely functionally related to rubrerythrin and ferredoxin. Analysis of the sequence conservation indicated that the wedge surface between the two domains are functionally important, interestingly, this area is part of dimer interface.
    The fold of this protein could best be described as a circularly permuted C2-like fold.

     

    Note from PFam: This protein is now in family DUF3501, PF12007.

    Dali structural search results:

    No:  Chain   Z    rmsd lali nres  %id  Description
       1:  2jnz-A  5.6  2.9   80   108    9   MOLECULE: PHL P 3 ALLERGEN;
       2:  1gyw-B  5.6  3.0   87   128    7   MOLECULE: ADAPTER-RELATED PROTEIN COMPLEX 1
       3:  2erj-B  5.3  3.1   85   204    7   MOLECULE: INTERLEUKIN-2 RECEPTOR ALPHA CHAIN;
       4:  2hcz-X  5.2  2.9   81   242   14   MOLECULE: BETA-EXPANSIN 1A;
       5:  1p4u-A  5.2  3.2   97   145   10   MOLECULE: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3;
       6:  1n10-A  5.2  2.9   78   228    9   MOLECULE: POLLEN ALLERGEN PHL P 1;
       7:  1bmw    5.1  2.6   77    94   12   MOLECULE: POLLEN ALLERGEN PHL P2;
       8:  3but-A  4.9  3.2   90   125    8   MOLECULE: UNCHARACTERIZED PROTEIN AF_0446;
       9:  3bpl-B  4.8  3.2   82   202    6   MOLECULE: INTERLEUKIN-4;
      10:  1rh8-A  4.8  3.6   98   142    8   MOLECULE: PICCOLO PROTEIN;
      11:  2o6c-A  4.7  3.2   94   158    6   MOLECULE: 34 KDA MEMBRANE ANTIGEN;
      12:  1w80-A  4.6  3.5   86   248    7   MOLECULE: ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2
      13:  2erj-C  4.5  3.4   84   195    5   MOLECULE: INTERLEUKIN-2 RECEPTOR ALPHA CHAIN;
      14:  1na8-A  4.4  3.2   85   151   13   MOLECULE: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1;
      15:  1gji-A  4.4  3.4   79   275    8   MOLECULE: C-REL PROTO-ONCOGENE PROTEIN;
      16:  3d33-A  4.2  3.1   73    94    7   MOLECULE: DOMAIN OF UNKNOWN FUNCTION WITH AN
      17:  3bes-R  4.2  3.1   74   250    8   MOLECULE: INTERFERON GAMMA;
      18:  2r51-A  4.2  3.4   89   288    7   MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26B;
     

    Figure 1. monomer of YP_111841.1

    monomer-pu10172a.png

    Figure 2. dimer of YP_111841.1

    dimer-pu10172a.png

    Figure 3. sequence conservation mapped onto surface (red=conserved)

    surface-pu10172a.png

     

    YP_111841.1 is similar to AAO38360 (GenBank) annotated as being induced under nitrogen fixation.

    It is the first structure from a protein family of over 100 proteins overrepresented in metagenomics data from Global Ocean Survey (see PSI-Blast result). The family is listed in PfamB as PB003488 but lacks functional annotation.

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
     dimer-pu10172a.png
    381695 dimer
    86.46 kB18:07, 26 Nov 2008qxuActions
     monomer-pu10172a.png
    381695 monomer
    57.27 kB18:07, 26 Nov 2008qxuActions
     surface-pu10172a.png
    381695 surface conservation
    94.67 kB18:07, 26 Nov 2008qxuActions
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