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The Open Protein Structure Annotation Network
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3oqq

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

    Title Crystal structure of a Putative lipoprotein (BACOVA_00967) from Bacteroides ovatus at 2.08 A resolution. To be published
    Site JCSG
    PDB Id 3oqq Target Id 417100
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS47437,ZP_02064008.1, 332527 Molecular Weight 48361.76 Da.
    Residues 434 Isoelectric Point 4.79
    Sequence nelekgndgsgtvdpvnastlvnvysdksgseasllvgdvlvkdsrtltlnvpaacekvymkyntvsgt eatkefalspvsrgvdqstgfnfetnrlasvtlalpedavqptnetdqgylfyhntgvvmfedgwpiql dswydedfndvvfeydlkvtechsqqmmetvggkeellltldvravggiyptvlgvvldglkseyvdri taslilkggqgtmtdlakeelstknivkvenknwnwsndtrkeprfailtvdkaqaegtvitldgltsl mdnnqdmfqvtqgkvreglpmlraevrligkegltgaerdaqlaafrelildtnrqnffikvnggkeih mrgyaptsaykaeyealvagdttldanvyysntkgstwgvklpvgtrhayervpfreaypdftkwvdsk gvsnqkwyenfvdektiryw
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.08 Rfree 0.2039
    Matthews' coefficent 2.48 Rfactor 0.1610
    Waters 301 Solvent Content 50.50

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    hypothetical protein BACOVA_00967 is cell surface protein, with close homologs mostly in Bacteriodes. It is partially [residues 37-261] similar to LruC of Leptospira interrogans serovar Pomona, LruC is one of immunoreactive leptospiral proteins. 

     

    Fig. 1 monomer

    sp16575d.png

     

    BACOVA_00967 structure has two domains, a small beta-barrel with an (almost) ig-fold on the N-terminus (see Figure 2 below) and another ig-like fold on the C-terminus (this one with significant extra elements in the loops, see Figure 3 below). These domains are founding members of two new Pfam families: DUF4841 (PF16129) and DUF4842 (PF16130), respectively.

     
     

     

    Fig. 2 Alignment and topology diagrams of the N-terminal domain of BACOVA_00967 (3oqq) in red and an ig-domain from TP47. Red boxes highlight the aligned elements of secondary structure. The alignment looks crummmy, but it has 52 equivalent positions with an RMSD of 3.09Å

    SP16575DNterm_d1o75a2_1_.pngScreen shot 2013-04-22 at 11.34.14 AM.png

     

    Fig 3. Alignment of the C-terminal domain of BACOVA_00967 (3oqq) in red and collagen-binding domain of adhesin from S. aureus (1amx). Note the extra loops and helices in the BACOVA_00967 (3oqq) structure. The alignment has 114 equivalent positions with an RMSD of 3.25Å.

    SP16575DCterm_d1amxa.png

     

     

    Fig. 4 mapping of conserved residues

     

    sp16575d-cons.png

     

    From pfam:

    This sequence hits one of our Pfam-Bs and so will be built as a DUF to start with. There are no other structures, so this might well be interesting.


    Update: I have built this and it overlaps with glycosyl-hydrolase_44, PF12891. So, I will close this ticket. (AG) - this cannot be, glycosyl-hydrolase_44, PF12891 is a TIM barrel hydrolase and BACOVA_00967 (3oqq) has a beta sandwich fold. Attempting to build a Pfam family again.

    Ligand Summary

    Reviews

    References

     

    No references found.

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