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

    Title Crystal structure of Putative lipid binding protein (YP_001304415.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution. To be published
    Site JCSG
    PDB Id 3jx8 Target Id 394796
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25372,YP_001304415.1, 325977 Molecular Weight 26876.68 Da.
    Residues 249 Isoelectric Point 5.08
    Sequence aadkridgngnpetreikisdydeitfvgsadfeyeqsdkapylsvtidenlfdylvteveggtlkiyp ksikkgfnnnsydlrptvykiksnskelkelntvgsgsfiiskptkvnrmeinmagsgnvelrgpvkgy klecnmagsgniiakdiqldnlscslassgeievigtvdrasfnvagsgeikafdcqarkaecniassg eisvyatqildanivgsgeihykgdpeisksimgsgsinkvk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 2.16 Rfree 0.210
    Matthews' coefficent 6.39 Rfactor 0.187
    Waters 1728 Solvent Content 80.76

    Ligand Information


    Google Scholar output for 3jx8
    1. Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint_based docking
    A Tuukkanen, B Huang, A Henschel, F Stewart - , 2010 - Wiley Online Library

    Protein Summary

    The gene BDI_3087 (YP_001304415) from Parabacteroides distasonis atcc 8503 encodesa protein that belongs to a large (over 350 members) PFAM family of proteins with unknown functions (DUF2807) found in gut, but also soil and marine Bacteroidetes, as well as (rarely) in other Gram-negative bacteria.  BDI_3087 is part of a cluster of four paralogs in Parabacteroides distasonis atcc 8503, a fifth paralog (BDI_0116) is located in other parts of a genome. JCSG is in the process of solving all of them. Similar number of paralogs are found in other Bacteroides, although clusters such as in P. distasonis are rare. JCSG now solved two additional structures from this family (3ljy and 3lyc).

    The three dimensional structure of BDI_3087 was deposited in PDB as 3jx8, it consists of right handed beta-helix, with statistically significant structural similarities to other right handed beta helix proteins such as the putative pectinase 3lyc (Dali Z-scr=31), pectate lyase (1ee6, FATCAT score 158; Dali Z-scr=12), filamentous hemaglutinin (2odl, Dali z-score 9.8) or P22 tailskike protein (2vfq, Dali z-score 9.5).  It shows a 44% secondary structure matching (SSM) with 1k8f, the C-terminal domain of the yeast adenyl cyclase associated protein. However, in most known right handed  beta helix proteins a superhelix turn consist of three or more beta strands or involves elongated loops. In contrast, one turn of the 3jx8 beta-helix is composed of a pair of parallel beta strands connected by tight turn, making it similar to the fold type of yersinia adhesin YadA collagen binding domain 1P9H, although YadA collagen binding domain adopts a left-handed beta-helix.  The same structural motif can be observed in the structure of the Bartonella adhesin BadA 3D9X.  

    Taken together, we hypothesize that BDI_3087 may belongs to the superfamily of trimeric autotransporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens [Ref] [Ref].  In the case of Parabacteroides distasonis, which are the normal distal human gut microbiota, TAA-like complexes most likely modulate adherence to the host. 


    Fig 1. 3jx8 dimer structure



    It is interesting to note that the sequence of BDI_3087 contains several well defined sequence repeats, centered around GSG motifs defining the tight beta turn between the two sheets of the super-helix. There are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two.



      kgyklecnmaGSGniiakdiqldn lscslasSGeievigt
       vdrasfnvaGSGeikafdcqark aecniasSGeisvyat


    Fig. 2. Positions of the GSG motifs (shown in blue) along the structure


    Ligand Summary




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