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    Table of contents
        1. 1.1.1. Protein Summary
    1. 2. Speculations:
        1. 2.1.1. Ligand Summary

    Title A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 A resolution. Acta Crystallogr.,Sect.F 66 1281-1286 2010
    Site JCSG
    PDB Id 3gf8 Target Id 393038
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20950,NP_809975.1, 324969 Molecular Weight 34213.72 Da.
    Residues 295 Isoelectric Point 4.75
    Sequence ascdsfnedlpecrlsvkfkydynmefadafhaqvdkvelyvfdkngkylfkqaeegsalstgnylmev elpvgqyqfmawagardsyditsltpgvstltdlklklkreasliinkrmetlwygevinvnfdgtvhq tetinlirdtkivrfgfqsytgswtldmndydyeiiesnghlghdnslldddvlsfrpyymeqkdpata yvdmntmrlmedrktrlvltekasgkrvfdinlidylamtnaegknlstqeyldrqsnyhiifflsesw lavqivvngwvhriqeenq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.20 Rfree 0.229
    Matthews' coefficent 3.25 Rfactor 0.189
    Waters 174 Solvent Content 62.16

    Ligand Information


    Google Scholar output for 3gf8
    1. Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families
    K Ellrott, L Jaroszewski, W Li, JC Wooley - PLoS computational , 2010 - dx.plos.org
    2. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron
    Q Xu, P Abdubek, T Astakhova, HL Axelrod - Section F: Structural , 2010 - scripts.iucr.org
    3. A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 A
    Q Xu, P Abdubek, T Astakhova, HL Axelrod - Section F: Structural , 2010 - scripts.iucr.org

    Protein Summary


    Bacteriodes thetaiotaomicron protein BT_1062 (target db id 393038) is a two domain, all-beta secreted protein which likely functions as a monomer. The structure of BT_1062 consists of  two beta sandwich domains with different, not readily alignable variants of the Greek key beta barrel topology. N-terminal domain has a prealbumin fold, found for instance in bacterial starch binding domain of beta-amylases (FATCAT alignment of an N-terminal domain of BT_1062 to the Starch-Binding Domain of Bacillus cereus B-amylase, PDB code 1cqy has an RMSD of 3.1 A with 15% sequence id). C-terminal domain has a topology similar to fibronectin III domain (FATCAT alignment to a second domain of the chain B of human interleukin 4 receptor, PDB code 1iar, has an RMSD of 3 A over 75 resiudes with a sequence id of 3.5%), but structural similarity to other sub-types of an immunoglobulin fold are also statistically significant.

    Interestingly, as DUF1812 is distantly related to a family of Porphyromonas gingivalis major fimbrial subunit protein (FimA), PF06321, which are virulence factors involved in adhesion to and invasion of host (human) cells, structure and functional prediction for BT_1062 suggests a possible mechanism of function for these important virulence factors.


    BT_1062 is a first representative of DUF1812 PF08842  family, large (close to 100 homologs) proteins specific to Bacteroides and present also in human gut metagenomic samples.


    LipPred (cleavage residue: 25) and LipoP (sequence SpII score=7.50643 margin=3.35388 cleavage=24-25 Pos+2=D) predicts it as bacterial lipoprotein. Asp at position +2 in relation to amino-terminal Cys, indicates that this protein is probably attached to the cytoplasmic membrane at the periplasmic side.


    Figure 1. monomer of 393038


    Figure 2. the conserved residues are mainly located near the domain interface








    Figure. FFAS03 server detects statistically significant similarity between BT_1062 and proteins from Pfam family PF06321.2, such as UniProt: FIMA4_PORGI encoding Porphyromonas gingivalis major fimbrial subunit protein (FimA), suggesting that both families are distantly homologous and may share some similarities in their functions.


    The C-terminal part of NP_809975.1 has structural similarity a wide range of proteins including PDB: 2nq3 (member  of C2-domain superfamily of proteins that often bind phospholipids in a Ca2+ dependent manner; SCOP sunid:49562). The same superfamily contains FimC.


    Proteins from FimA and FimC families are involved in fibre assembly through the chaperone-usher pathway [Vetsch et al. 2006, Fronzes at al 2008].

    Ligand Summary




    No references found.

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    Files (3)

    FileSizeDateAttached by 
    gs13834 consurf1
    218.52 kB19:33, 6 Mar 2009qxuActions
    gs13834 consurf2
    187.38 kB19:33, 6 Mar 2009qxuActions
    393038 monomer
    81.02 kB23:40, 2 Feb 2009qxuActions
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