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

    Title Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron. Acta Crystallogr.,Sect.F 66 1297-1305 2010
    Site JCSG
    PDB Id 3kk7 Target Id 393005
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20928,NP_812351.1, 324986 Molecular Weight 61368.55 Da.
    Residues 540 Isoelectric Point 5.30
    Sequence neeetnnytpvdnqsnstseiilqernsslprvwskktaqrvttrasftdatdflgcsyavengtsiig dfanakypvvnmkkllerypsyinpkelrttetkalsysdfdrleknktftktvksgfslnlgpfkfgr qktiketfvhntddsekvvhgelsievvngmlnlqtapsalrkiaadyldelfvdalynssmvelmqsy gefvltgyytggrasalfygvdtnsiqfdskekdmdvainasyewknkkptapsdtihsasgnlsigtk rensetitnkfsalsysiktlggaygysistppyditnysidltpwlqslndpkthtmidlqdgglypi sdfileenfkqryndthmdfqyqesleepyieiikmyirksnsgeklydivpvlntrqgdklifsnpda asqsdeelkansipatfltksnaikdekskyyqlkikadpnktinpiiqttlsfqinnvdekgmykfkn antniwyiynptsmycfayydddyipdaygildwvngipikavtmttlyqrykiygl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.46 Rfree 0.252
    Matthews' coefficent 2.78 Rfactor 0.209
    Waters 239 Solvent Content 55.74

    Ligand Information


    Google Scholar output for 3kk7
    1. Dali server: conservation mapping in 3D
    L Holm, P Rosenstrm - Nucleic acids research, 2010 - Oxford Univ Press
    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. TOPSAN: a dynamic web database for structural genomics
    K Ellrott, CM Zmasek, D Weekes - Nucleic acids , 2011 - Oxford Univ Press
    4. Quantifying instrument errors in macromolecular X-ray data sets
    K Diederichs - Acta Crystallographica Section D: Biological , 2010 - scripts.iucr.org
    5. Packing a punch: the mechanism of pore formation by cholesterol dependent cytolysins and membrane attack complex/perforin-like proteins
    MA Dunstone, RK Tweten - Current Opinion in Structural Biology, 2012 - Elsevier

    Protein Summary

    The structure of the protein encoded by Bacteroides theraiotaomicron gene BT_3439 (NP_812351.1) is the first representative of a new family (weak hit (E-value 0.91) with DUF1160). The structure reveals a MACPF N-terminal domain and an extra C-terminal domain, that could be further divided into three smaller domains. The top hit in SSM is 2qp2, a bacterial perforin-like protein, with 41% of secondary structure elements (SSE) matching. HHpred top hits are MACPF domains 2qp2 (E-value 4.7E-23) and 2rd7 (E-value 3.3E-18). All three hits are corroborated by Dali with Z-scores of 17.4, 12.9 and 12.3 for 2qp2, 2rd7 and 2qqh, respectively. The C-terminal domain (residues 389-528) does not have a significant match to known proteins.


    The MACPF domain is involved in human complement activation and bacterial attack [Ref][Ref]. This structure is the second MACPF domain from bacteria (pdb 2qp2) and third MACPF structure [Ref]. MACPF domain is also present in human complement component C8 alpha chain (PDBs 2qqh, 2rd7).


    MACPF domain  (Membrane Attacking Complex) is known to form pores inside membranes.


    Figure 1. Structure of BT3439


    In is interesting to note, that BT_3439 is strongly upregulated in all host-associated, but not in in vitro growing conditions of B. thetaiotaomicron, as shown by the expression data from Jeff Gordon's lab (http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS1849)[Ref]. Expression is further increased in the presence of a simple sugar (versus polysaccharide) diet.


    STRING (http://string.embl.de) predicts a functional association of BT_3439 with BT_3438, BT_3440 and BT_3441, all putative uncharacterized proteins. A cross-check with the expression data for these genes shows an identical expression profile for BT_3440 and BT_3441 and a similar one for BT_3438, in agreement with the hypothesis that these proteins may form a functional unit. Remote homology analysis reveals that BT_3440 shows significant homology with toxins (PF03318, FFAS score -36.0 and PF01117, FFAS score -25.1) further indicating that this functional unit acts as an invasion complex.



    Ligand Summary




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