.
The Open Protein Structure Annotation Network
PDB Keyword
.

3gf8

    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
    Ligands
    Metals

    Jmol

     
    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

    GS13834a.png

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

    consurf1.png

    consurf2.png

     

    Speculations:

     

     

    39 VKFKYDYNMEFADAFHAQVDKVELYVFDKNGKYLFKQAEEGSALSTGNYLMEVELPVG-QYQFMAWAGARDSYDITSLTPGVSTLTDLKLKLKREASLII 137
     2 IIKSGEGRAVGDGLADAKITKLTAMVYAGQIQ---EGIKTVEEADGVLKVEGIPCKSGANRVLVVVANHNYELTGKSLNEVEALTTSLTAENQNAKNLIM 98
    
    138 NKRMETL-------WYGEVINVNFDGTVHQTETINLIRDTKIVRFG-FQSYTGSWTLDMNDYDYE------IIESNGHLGHDNSLLDDDVLS-------- 215
     99 TGKSAAFTIKPGSNHYGYPDGTTSDNLVSAGTPLAVTRVHAGISFAGVEVNMATQYQNYYSFNPADAKIAALVAKKDSKIFGNSLVSNTNAYLYGVQTPA 198
    
    215 ----------------------------FRPYYMEQKDPATAYVDMNTMRLMEDRKTRLVLTE-----------KASGKRVFDINLIDYLAMTNAEGKNL 276
    199 GLYTPDAAGETYELEASLNTNYAVGAGFYVLESKYDASNELRPTILCIYGKLLDKDGNPLTEPALTDAINAGFCDGDGTTYYPVLVNYDGNGYIYSGAIT 298
    
    277 STQEYLDRQSNYHIIFFLS-------------ESWLAVQIVVNGWVHRIQEE 315
    299 QGQNKIVRNNHYKITLNITGPGTNTPENPQPVQANLNVTCQVTPWVVVNQAA 350

    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

    Reviews

    References

     

    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
     consurf1.png
    gs13834 consurf1
    218.52 kB19:33, 6 Mar 2009qxuActions
     consurf2.png
    gs13834 consurf2
    187.38 kB19:33, 6 Mar 2009qxuActions
     GS13834a.png
    393038 monomer
    81.02 kB23:40, 2 Feb 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