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3ke7

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

    Title Crystal structure of putative ketosteroid isomerase (YP_001303366.1) from Parabacteroides distasonis ATCC 8503 at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3ke7 Target Id 385935
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25710,YP_001303366.1, 3.10.450.50 Molecular Weight 15566.96 Da.
    Residues 133 Isoelectric Point 4.78
    Sequence qqknmenktlnenipemiislekealastdpmafvelsdtdviyfdpsletkiegleqlrtyykgmqlp padhfdmirpvvqvaqniavltfnldsylsdkvikwnctevyrrnpdnqwkiiqthwsyvkpld
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.45 Rfree 0.182
    Matthews' coefficent 1.83 Rfactor 0.152
    Waters 267 Solvent Content 32.74

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ke7
    1. Quantifying instrument errors in macromolecular X-ray data sets
    K Diederichs - Acta Crystallographica Section D: Biological , 2010 - scripts.iucr.org
     

    Protein SummaryTT

    Target YP_001303366.1 (15.6 kDa, 154-residues) is annotated as hypothetical protein BDI_2009 from Parabacteroides distasonis, an anaerobic bacteria that is prevalent in mammalian intestinal flora.  The protein has been classified as belonging to the bacterial sugar transferase Pfam (PF02397).

    The structure of an N-terminally truncated 133-residue long version of YP_001303366.1 (residues 22-154) was solved by the Se-MAD method to a resolution of 1.45 Angstroms, the first structure for this Pfam.  The structure adopts an alpha-beta fold that is classified by fastSCOP as belonging to the nuclear transport factor 2 (NTF2)-like superfamily in the SCOP database (Figure 1a). 

    YP_001303366.1 assembles as a dimer in the crystallographic asymmetric unit (Figure 1b),  an oligomeric state which is supported as being the physiologically relevant form by PISA crystallographic packing analysis.

    Figure 1.  (a) structure of a monomer of YP_001303366.1 gradiently colored from N- (blue) to C-terminus (red).  (b) structure of the putative physiologically relevant dimeric form of YP_001303366.1 (chain A in yellow, chain B in blue).

    GS13562A-monomer.png  GS13562A-dimer.png

     

    DALI and SSM searches result in the top structural homologs mostly being nuclear transport factor 2 proteins (Tables 1 and 2).

    Table 1.  Top structural homologs from DALI search.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1zx2 15.5 2.2 120 130 9 UBP3-ASSOCIATED PROTEIN BRE5
    2 1u5o 15.0 2.8 120 125 5 NUCLEAR TRANSPORT FACTOR 2
    3 1qma 14.9 2.5 118 124 5 NUCLEAR TRANSPORT FACTOR 2
    4 1oun 14.9 2.3 116 121 5 NUCLEAR TRANSPORT FACTOR 2
    5 1ar0 14.9 2.5 117 121 5 NUCLEAR TRANSPORT FACTOR 2
    6 2qiy 14.8 1.9 115 134 10 UBP3-ASSOCIATED PROTEIN BRE5
    7 1zo2 14.8 2.2 115 124 10 NUCLEAR TRANSPORT FACTOR 2
    8 1jb5 14.8 2.4 117 123 4 NUCLEAR TRANSPORT FACTOR 2
    9 1jb2 14.8 2.5 117 123 5 NUCLEAR TRANSPORT FACTOR 2
    10 1gy6 14.8 2.6 119 123 5 NUCLEAR TRANSPORT FACTOR 2

     

    Table 2.  Top structural homologs from SSM search.

    N PDB Q-score RMSD TITLE
    1 1jb5 0.5581 1.799 NTF2 M118E MUTANT
    2 1zo2 0.557 1.839 STRUCTURE OF NUCLEAR TRANSPORT FACTOR 2 (NTF2) FROM CRYPTOSPORIDIUM PARVUM
    3 1ask 0.5524 1.856 NUCLEAR TRANSPORT FACTOR 2 (NTF2) H66A MUTANT
    4 1gy5 0.5509 1.903 D92N,D94N DOUBLE POINT MUTANT OF HUMAN NUCLEAR TRANSPORT FACTOR 2 (NTF2)
    5 1qma 0.5452 1.851 NUCLEAR TRANSPORT FACTOR 2 (NTF2) W7A MUTANT
    6 1jb2 0.5451 1.755 NTF2 M84E MUTANT
    7 1ar0 0.545 1.812 NUCLEAR TRANSPORT FACTOR 2 (NTF2) E42K MUTANT
    8 1oun 0.5447 1.751 NUCLEAR TRANSPORT FACTOR 2 (NTF2)
    9 1gy6 0.5401 1.910 NTF2 FROM RAT, AMMONIUM SULPHATE CONDITIONS
    10 2w2c 0.5387 1.542 STRUCTURE OF THE TETRADECAMERIC OLIGOMERISATION DOMAIN OF CALCIUM-CALMODULIN DEPENDENT PROTEIN KINASE II DELTA

     

    Superposition of a monomer of YP_001303366.1 with several nuclear transport factor 2 (NTF2) structural homologs (Figure 2a) shows close structural similarity among the monomers; however, YP_001303366.1 and the structural homologs differ in their dimer arrangement (Figure 2b), and the residues that are deemed to be functionally important in the structural homologs are not conserved in YP_001303366.1.  These differences are not surprising considering that ubiquination and nuclear transport, processes which these structural homologs play a role in eukaryotes, are absent in prokaryotes such as Parabacteroides distasonis.

    Figure 2.  (a) Superpostion of YP_001303366.1 monomer (yellow) with monomers of structural homologs 1zx2 (green), 1u5o (cyan), and 1jb5 (magenta).  (b)  Superposition of monomer A (shown as cartoon loop) of YP_001303366.1 (yellow) and 1zx2 dimer (green) reveals different dimer arrangements, as can be seen from the different positioning of monomer B (shown as cartoon ribbons and helices) with respect to monomer A.

    (a)                                                                                        (b)

    GS13562A-superpose.png   GS13562A-1zx2.png

     

    A ConSurf analysis of YP_001303366.1 reveals that the most highly conserved residues are located at the core of the dimer, on the beta-strands which form the dimer interface (Figure 3a).  One of these highly conserved residues (Asp-67) is located at the bottom of a deep surface cleft in which a bicine molecule is bound.  It is possible that any existant active site could perhaps be located in this region (Figure 3b)

    Figure 3.  ConSurf analysis of YP_001303366.1.  (a) Residue conservation is mapped onto monomer A (left) and shows that the majority of conserved residues are located at the core of the dimer.  (b) YP_001303366.1 contains a deep cleft at the surface that could perhaps be the active site.  A bicine (green sticks) is bound in this region, near a highly conserved aspartate (Asp-67).

     

    (a)                                                                                        (b)

    GS13562A-consurf.png   GS13562A-consurf-2 (1).png

     

     consurf_legend.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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