The Open Protein Structure Annotation Network
PDB Keyword


    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 394828
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25396,YP_001302526.1, 325969 Molecular Weight 55255.55 Da.
    Residues 505 Isoelectric Point 5.60
    Sequence aaseaeygkvskawtlhadgsqeyrssmeltlfthtamnstygesfivynpdfqtlkihssytrqkdgt ivktpdnafvevlprfaadapaynqlkemvvvhtglelgatiyldysiitkpgyypaldinerlqetsp vkeckvsisvpegtplacglygspvkaveeshdgikevhwtlrnipassreafqpknreasphlvasty psgkaalatldkrlkesqgyesktfaqfltdksgneqekvniirdhilnnlstcpipmamtgytvrdid tvlrsaygtpleiaqllnvmlnaagipsevlavypghldtdacglaaiqtlavkatvdgkdqylsaspl tnrggldkvvslsgtsieiettpiqikesrsvaisadqakdgfaicvlpaisagidswgmsalnskrsn lfelpslireevtytvtpaegmklqtstqeqviskpfgkvtrtitprgntievvrtielnkqqftpaey sdvrslihewtnpdnrvllfsl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.00 Rfree 0.200
    Matthews' coefficent 4.28 Rfactor 0.170
    Waters 1095 Solvent Content 71.27

    Ligand Information


    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

    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


    Figure 2. mapping of conserved residues on the protein surface


    Ligand Summary




    No references found.

    Tag page
    • No tags

    Files (3)

    FileSizeDateAttached by 
    gs8421 surface conservation 1
    170.46 kB05:34, 23 Oct 2009qxuActions
    gs8421 surface conservation 2
    102.57 kB05:34, 23 Oct 2009qxuActions
    gs8421a monomer
    107.91 kB21:54, 15 Sep 2009qxuActions
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch