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The Open Protein Structure Annotation Network
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3n6z

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

    Title Crystal structure of a putative immunoglobulin A1 protease (BACOVA_03286) from Bacteroides ovatus at 1.30 A resolution. To be published
    Site JCSG
    PDB Id 3n6z Target Id 416733
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS33828,ZP_02066290.1, 384458 Molecular Weight 37631.63 Da.
    Residues 362 Isoelectric Point 4.90
    Sequence iscsdpnpldsytrvpfektetddgngdgdgdgagglfekgngtdskpymimnatqirnmrsvlksgmk vyfqlgadidmagiddwqslngsgdfpyeidfdgdshviknfkcsagdypsffgvlcgdcrnvgfvnas vssarqgigiitgylglkdkgngnktgrivncyttgevigsgaaggiagvlansydgqesyikncysna tvsdraasggkaggiagrkvgvggfiencyaygavsatkggvggilgqidkscdiaiknsaawsnltgv dasstvgrivgvsaslgsyencyacesivlkvnektitasdessatgttfhgvaksaeelgniivawnp nlwkkgtngypifqwse
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.30 Rfree 0.157
    Matthews' coefficent 2.49 Rfactor 0.135
    Waters 463 Solvent Content 50.63

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3n6z
    1. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     
    2. Fragment Finder 2.0: a computing server to identify structurally similar fragments
    R Nagarajan, S Siva Balan, R Sabarinathan - Journal of Applied , 2012 - scripts.iucr.org
     

    Protein Summary

    hypothetical protein BACOVA_03286 is a single domain protein with statitically significant similarity to the N-terminal half of  Pfam Peptidase_M26_N domain, it also shows a more distant relation to the Glug repeats. Glug repeats are often involved in adhesion. The structure forman an unusual right-handed beta helix which has not been seen before to our knowledge. It consists of a series of repeats seen both in structure and in sequence (Fig 2). 

     

    The significance of matching between this protein and Glug domains has yet to be explored.

     

    Fig 1. structure of  BACOVA_03286

    sp13881e.png

     

    Fig.2. Sequence repeats in BACOVA_03286, seen as lines parallel to the main diagonal in the lower right side of the picture (experimenal FFAS-RR (repeat recognized)).

    a.aver5.l0.jpeg

     

    Interestingly, this domain can be found in several domain arragnements, as a:

    - in single domain proteins (rarely) or duplicated in two domain proteins (more often) - both only in Bacteroidetes 

    - in immunoglobulin A1 proteases, as the C-terminal half of the Pfam Peptidase_M26_N domain - mostly in various Streptococcus species

    at the N-terminal domain of S-layer proteins, followed by S-layer domains (in these proteins some of the repeats in the N-terminal domain are recognized as GLUG-motifs) -mostly in different Paenibacillus  species

    Probably, the definition of the Pfam Peptidase_M26_N domain is incorrect - the N-terminal half of this domain is the actual protease domain, while the C-terminal half should should become a part of the a new domain, covering our structure. It is tempting to speculate that this domain plays a role similar to the autotransporter domain in other (nonhomologous!)  immunoglobulin A1 proteases, such as for instance Haemophilus influenzae Immunoglobulin A1 Protease (3h09). Immunoglobulin A1 proteases can typically consist of autotransporter and a passanger domains. To continue our speculation, since in Bacteroides these domains can be found alone, they could form some kind of new transport system

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

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     a.aver5.l0.jpeg
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    178.49 kB23:32, 6 Sep 2013adamActions
     sp13881e.png
    SP13881E
    123.13 kB16:16, 19 May 2010qxuActions
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