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3up9

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

    Title Crystal structure of a hypothetical protein ACTODO_00931 (hypothetical protein ACTODO_00931, SP17422A, P_02044074.1) from Actinomyces odontolyticus ATCC 17982 at 2.35 A resolution. To be published
    Site JCSG
    PDB Id 3up9 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS66363,ZP_02044074.1, 327257
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 4.08 Rfactor 0.1565
    Waters
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    Solvent Content 69.83

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3up9

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    Protein Summary

    The  hypothetical protein ACTODO_00931 (ZP_02044074.1) is a member of the PFAM PF03180 Lipoprotein_9family. It is closely homologous (~30% seq id) to four lipoproteins with solved structures (1xs5, 3k2d, 3gxa, 1p99). Interestingly, three of those are from Gram negative bacteria (Treponema pallidum, Vibrio vulnificus and Neisseria meningitidis, respectively, the fourth one, 1p99 is from Gram positive  Staphylococcus aureus ), while ours is from a Gram positive Actinomyces odontolyticus. What I still dont understand is that these three are often referred to as being immunogenic, while at he same time being called periplasmic binding proteins, which would imply they are located in the periplasm, i.e would be unavailable to antibodies. For instance in the 3GXA paper they write "GNA1946, a conserved outer membrane lipoprotein from Neisseria meningitidis, has been identified as a candidate antigen for an urgently needed broad-spectrum meningococcal vaccine. It has been predicted to be a periplasmic receptor in the D-methionine uptake ABC transporter system. " So is it outer-membrane or periplasmic?

    Our protein, given that it comes from a Gram positive bacterium, is clearly an outer membrane protein.

     

     

    The monomer structure is shown below.

    SP17422A.png

     

    There is a Methionine residue bound in the core of the protein, like the closest homolog structure 3tqw. A close up view of the Met binding site is shown below, with surrounding 2FoFc density.

    SP17422A_MET_density.png

     

     

    The top 10 DALI homologs are shown below in the table.

    N PDB Z-score RMSD LALI NRES %ID Description
    1 3tqw 31.6 1.7 231 234 32 Methionine-binding Protein
    2 1xs5 31.4 1.8 235 240 32 Membrane Lipoprotein Tpn32
    3 3k2d 29.6 1.9 228 238 29 Abc-type Metal Ion Transport System, Periplasmic
    4 1p99 29.5 1.8 232 255 29 Hypothetical Protein Pg110
    5 3gxa 29.1 1.9 231 240 31 Outer Membrane Lipoprotein Gna1946
    6 3ir1 29.0 1.9 231 240 31 Outer Membrane Lipoprotein Gna1946
    7 3gzg 15.4 3.8 207 232 12 Molybdate-binding Periplasmic Protein Permease
    8 2h5y 15.2 3.8 208 233 12 Molybdate-binding Periplasmic Protein
    9 1amf 15.1 4.0 207 231 11 Molybdate Transport Protein Moda
    10 1wod 15.0 4.0 207 231 11 Moda

     

    A superposition of this structure (green) on 3tqw (blue) is shown below. The ligand (Methionine) gets superposed perfectly as well.

    SP17422A_3tqw.png

     

    A closer look at the binding site reveals that the binding site has a high degree of residue conservation. This suggests that these proteins might share the function, namely ABC transporter.

     

    SP17422A_3tqw_conserved.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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