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The Open Protein Structure Annotation Network
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3h4q

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

    Title Crystal structure of putative acetyltransferase (NP_371943.1) from STAPHYLOCOCCUS AUREUS MU50 at 2.50 A resolution. To be published
    Site JCSG
    PDB Id 3h4q Target Id 378017
    Molecular Characteristics
    Source Staphylococcus aureus subsp. aureus mu50
    Alias Ids TPS7032,NP_371943.1, BV1424C, 335757 Molecular Weight 19845.34 Da.
    Residues 169 Isoelectric Point 4.53
    Sequence mirlgkmsdldqilnlveeakelmkehdneqwddqypllehfeediakdylyvleendkiygfivvdqd qaewyddidwpvnregafvihrltgskeykgaatelfnyvidvvkargaeviltdtfalnkpaqglfak fgfhkvgeqlmeyppydkgepfyayyknlke
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.50 Rfree 0.253
    Matthews' coefficent 3.20 Rfactor 0.219
    Waters 21 Solvent Content 61.60

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3h4q

    Protein Summary

    This is a protein of unknown function annotated under the Pfam GNAT family of acetyltransferases, PF00583.

    The structure shows a 7-stranded beta-sheet flanked by several alpha-helices on both sides:

    Fig1.png

    The structure is similar to many other acetyltransferases (as found by SSM), for example, those with PDB accession ids: 2fia(Q-score 0.53, rmsd of 1.49A over 123 aligned Ca, sequence identity of 26%, Midwest Center for Structural Genomics) and 2pc1(Q-score 0.53, rmsd of 1.80A over 134 aligned Ca, sequence identity of 26%, Joint Center for Structural Genomics, Topsan link to target 371586, protein NP_688560.1). These two proteins are also among the very top hits in the FFAS results (link above).

    Of the 5 top similar strutures found by SSM, 4 have been determined by structural genomics initatives.

    The fifth most similar structure is that of the Rimi protein GNAT acetyltransferase that is responsible for the Nalpha-acetylation of ribosomal protein S18 in Salmonella typhimurium (PDB id 2cns, Q-score 0.46, rmsd of 1.86A over 118 aligned Ca, sequence identity of 15%, Ref1).

    Based on structural comparison of this protein (green, below) to the 2cns protein (cyan, below) which has bound CoA (pink, below), the CoA binding site for this protein may be as follows:

    Fig2_superimposedon2CNS.png

    During crystallization, 1mM acetyl-CoA was added to this protein, but it did not co-crystallize. This could be due to the difference in the loop conformation in the putative CoA binding site which could have prevented the co-crystallization.

    However, we do see some density modeled as a UNL near residues Asn129 and Arg91 which is in between the characteristic motifs A & B (of motifs A, B, C and D) of GNAT acetyltransferases. These residues are conserved across many of the similar proteins as can be seen from the FFAS results. The UNL (red spheres) in the final 2Fo-Fc map (blue, 1.0 sigma contour) and Fo-Fc (green, 3.0 sigma) is shown:

    UNL.png

    GNAT acetyltransferases usually have a conserved "P-loop" that coordinates with the pyrophosphate moiety of the acetyl-CoA. For details on which residues are involved in this, refer Ref1 and sequence alignments via the FFAS server, linked above).

    We (JCSG) have also solved 2 other crystal structures of GNAT family proteins which do not come up in the SSM hits but one of them is in the top FFAS hits, PDB ids 2oh1 from Listeria monocyotgenes, TOPSAN link, and 2aj6 from another strain of Staphylococcus aureus MW2, TOPSAN link). Both of them have an uindentified ligand (UNL) bound. Since all 3 proteins, this one and the 2oh1 and 2aj6 are from pathogenic organisms, it may be interesting to further explore the biochemistry of these 2 proteins.

    If we compare the UNL bound in this protein (UNL in black, protein in green) with the 2oh1 (UNL in blue, 1oh1 in magenta) and the UNL in the 2aj6 (UNL in red, 1aj6 in yellow) by superimposing on the 2cns (acetyl-CoA in pink, 2cns in cyan)structure above, we can get an idea of the binding sites in these proteins:

    UNLon2oh12aj62cns.png

     These UNLs can provide clues about possible substrates and inhibitors. The variation in the binding sites is interesting and may be affect protein function.

     

    References:

    1. Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N(alpha)-acetylation of ribosomal protein S18. Vetting MW, Bareich DC, Yu M, Blanchard JS. Protein Sci. 2008 Oct;17(10):1781-90.

    Ligand Summary

    A UNL (Unidentified Ligand) has been modeled in the region of the putative active site.

    Reviews

    References

     

    No references found.

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