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3kd4

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

    Title Crystal structure of Putative proteases (YP_001302526.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3kd4 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS25396,YP_001302526.1, 325969
    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 4.28 Rfactor 0.170
    Waters
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    Solvent Content 71.27

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3kd4
    1. Structural characterization of a conserved, calcium-dependent periplasmic protease from Legionella pneumophila
    D Chatterjee, CD Boyd, GA O'Toole - Journal of , 2012 - Am Soc Microbiol
     

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    Protein Summary

    Protein BDI_1141 from Parabacteroides distasonis is a putative exported protein with no known function. It consists of 3 domains (23-229, 230-388, 389-527). Full length homologs are found only in  Bacteroides and BDI_1141 is the first protein with a solved structure that has all three domains. Although the sequence anotation indicated that this protein might bind GTP/ATP, however, the rational behind this annotation is not clear. The genomic neighborhood seems to indicate a possible role in carbohydrate (Glycosaminoglycan?) metabolism. Its upstream neighbor is a protein that also contains a transglutaminase core, the downstream neighbor is  a putative hyaluronoglucosaminidase.

     

    The first domain is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase (3ebi, Z=10, rmsd 3.6A for 152 CA, seq id 12%), despite lack of any significant sequence similarity. The second, central domain is a first structural representative of the PFAM Transglutaminase-like domain (PF04473 and PF04473--formerly called DUF553), which is confirmed by a structure similarity to already solved proteins representing other families from the Peptidase_CA clan, for instance to a putative cysteine peptidase ( 3isr, Z=10.1, rmsd 2.8A for 118 aligned Ca, seq id 19%). The third domain is similar to part of neuropilin-2 (Z=4.6, rmsd 3.6A for 83 CA, 7% seq id). Domains 2 and 3 appears to be part of  peptide-n-glycanase (1x3w & 2g9f).

     

    The most conserved residues are almost all mapped to the first domain, indicating this is the most important of this molecule (protein docking site?). The conserved residues on surface on domain 2 are also sit next to this site. No active site could be found in BDI_1141. Thus, it appears that BDI_1141 is part of a protein complex with possible activity in carbohydrate metabolism.

     

    Figure 1. 394828 monomer

    gs8421a.png

    Figure 2. mapping of conserved residues on the protein surface

    gs8421a-conv2.pnggs8421a-conv1.png

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
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    Files (3)

    FileSizeDateAttached by 
     gs8421a-conv1.png
    gs8421 surface conservation 1
    170.46 kB05:34, 23 Oct 2009qxuActions
     gs8421a-conv2.png
    gs8421 surface conservation 2
    102.57 kB05:34, 23 Oct 2009qxuActions
     gs8421a.png
    gs8421a monomer
    107.91 kB21:54, 15 Sep 2009qxuActions
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