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3uws

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

    Title Crystal structure of a hypothetical protein (PARMER_00083) from Parabacteroides merdae ATCC 43184 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3uws Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS66835,ZP_02030115.1
    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 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.02 Rfactor 0.1428
    Waters
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    Solvent Content 38.96

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3uws

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    Protein Summary

    Pfam update: Peptidase_C11, Clostripain family Family CL0093 bit-score=184.8, evalue=2e-54.

    It's classified in the Pfam family PF03415 (Peptidase_C11, Clostripain) with about 200 unique proteins and this is the first structural representative.

    It is in the Peptidase_CD clan with 7 other families.


    The family includes 138 species found in eukaryotes, bacteria (predominant, 121/138 species) and archae.


    Amongst the bacteria, it is predominant in gut bacteria, with ~50% in bacteroidetes.


    In the majority of the 200 proteins in this family, 165 are proteins which just cover this Peptidase_C11 only, without other accessory domains.

    The most interesting feature in both chains is the lack of residue K147 in the sequence NKLKAFG, which really corresponds to a large spatial gap of ~16 A in the polypeptide chain from this single missing residue.

    Mass spectrometry indicates cleavage of the protein after K in the sequence KAFG and this is confirmed by the crystal structure (the ends are in red below)

    The protein is annotated as belonging to the clostripain family of endopeptidases. Clostripain is usually associated with cleavage of the peptide bond after a arginine residue. It appears that it can also recognize lysine for cleavage but with lower efficiency. It could be that the gap seen in the structure is due to some autocleavage.

    The 2 catalytic residues (based on homology) are likely to be Cys179 and His133 (in stick figures below) that are part of the separate segments after cleavage and so the two chains probably come together to form the active site.

    SP5111Einitial_102711.png

    Further sequence-structure-function analysis will be added.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    303.01 kB18:23, 7 Nov 2011debanuActions
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