.
The Open Protein Structure Annotation Network
PDB Keyword
.

3kog

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

    Title Crystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution. To be published
    Site JCSG
    PDB Id 3kog Target Id 393242
    Molecular Characteristics
    Source Bacteroides vulgatus atcc 8482
    Alias Ids TPS24859,YP_001301288.1, 324148 Molecular Weight 27594.96 Da.
    Residues 255 Isoelectric Point 5.10
    Sequence scekenigievtpvnakfiitpvvidattgtdvtqsaeisfskgngtyegtpelasesininakykgmt gsasvtipalkagqfgakevtiilsenffaqeessnsqiettkhsgfknntsdywyyitvtytkkegse vikndyegddseikniidaynkgvredkvtlndvqvlahsrfsvfvdymkttsvyqiiekspkrdgnpv asftvdsyntivspkneqipghghapshghghghgddsnagggiiiad
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.85 Rfree 0.214
    Matthews' coefficent 2.20 Rfactor 0.182
    Waters 171 Solvent Content 44.11

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3kog
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    Protein BVU_4064 (JCSG target ID 393242, JCSG target accession code GS13738A, GenBank accession code YP_001301288.1) is a 282-amino acid long protein from Bacteroides vulgatus, an anaerobic, gram-negative bacterium that is a prevalent member of the human intestinal flora.  The protein is annotated as a hypothetical protein and has not been assigned to a Pfam.

    The structure of an N-terminally truncated version of BVU_4064 (residues 28-282), solved by the Se-Met multi-wavelength anomalous dispersion (MAD) method to a resolution of 1.85 Angstroms, consists of an N-terminal domain (residues 39-122) and a C-terminal domain (residues 123-266) that are predominantly beta in structure (Figure 1).  

    Figure 1.  (a)  Structure of BVU_4064 gradiently colored from the N- (blue) to the C-terminus (red).  (b) The N-terminal (green) and C-terminal (purple) domains of BVU_4064.  (c)  same as in (b) except rotated by 90 degrees about the vertical axis.  MPD molecule is represented as yellow sticks in all three panels.

    (a)                                                        (b)                                                        (c)

    GS13738A_gradient.png         GS13738A_domains_1.png      GS13738A_domains_2.png

     

    Top hits from a Dali search  are listed in Table 1.  A search using FATCAT yielded similar results, with the top three hits being 1uyj, 3g3l, and 3e8v.

    Table 1.  Structural homologs of BVU_4064 as assessed by Dali (structures that are highlighted are shown superimposed with BVU_4064 in subsequent figures).

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3g3l 8.7 4.0 174 291 16 PUTATIVE UNCHARACTERIZED MEMBRANE-ASSOCIATED (TOPSAN)
    2 1uyj 5.3 3.5 129 273 6 EPSILON-TOXIN (Cole et al. 2004)
    3 1w3g 4.6 4.4 118 312 5 HEMOLYTIC LECTIN FROM LAETIPORUS SULPHUREUS (Mancheño et al. 2005)
    4 1w3f 4.6 4.4 118 312 5 HEMOLYTIC LECTIN FROM LAETIPORUS SULPHUREUS
    5 3e8v 4.3 1.7 59 82 24 POSSIBLE TRANSGLUTAMINASE-FAMILY PROTEIN
    6 2ztb 4.2 6.0 120 247 9 CRYSTAL PROTEIN
    7 2d42 4.2 5.0 124 249 9 NON-TOXIC CRYSTAL PROTEIN
    8 1w3a 4.2 4.0 112 312 4 HEMOLYTIC LECTIN LSLA
    9 1qmu 4.1 3.5 70 380 23 CARBOXYPEPTIDASE GP180 RESIDUES 503-882

     

    Structural neighbor searches were also done using only either the N-terminal or the C-terminal domain of BVU_4064 in the query, the results of which are shown in Tables 2 and 3, respectively.  The top hits resulting from these searches were also hits in the searches using the entire protein in the query.

    Table 2.  Structural homologs of the N-terminal domain of BVU_4064 as assessed by Dali.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3e8v 6.6 1.7 59 82 24 POSSIBLE TRANSGLUTAMINASE-FAMILY PROTEIN
    2 1h8l 6.3 3.4 69 380 23 CARBOXYPEPTIDASE GP180 RESIDUES 503-882
    3 1qmu 6.2 3.4 69 380 23 CARBOXYPEPTIDASE GP180 RESIDUES 503-882
    4 2nsm 5.9 3.4 69 390 19 CARBOXYPEPTIDASE N CATALYTIC CHAIN
    5 1ti4 5.3 3.1 66 274 15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT
    6 1ti6 5.2 3.1 66 274 15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT
    7 1vlf 5.1 3.1 66 274 15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT
    8 1vle 5.1 3.1 66 274 15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT
    9 1vld 5.1 3.1 66 274 15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT
    10 1ti2 5.1 3.1 66 274 15 PYROGALLOL HYDROXYTRANSFERASE LARGE SUBUNIT

     

    Table 3.  Structural homologs of the C-terminal domain of BVU_4064 as assessed by Dali.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1uyj 6.9 3.5 128 273 6 EPSILON-TOXIN
    2 1w3g 6.6 4.9 121 312 7 HEMOLYTIC LECTIN FROM LAETIPORUS SULPHUREUS
    3 1w3f 6.4 5.2 122 312 7 HEMOLYTIC LECTIN FROM LAETIPORUS SULPHUREUS
    4 1w3a 5.9 5.1 118 312 6 HEMOLYTIC LECTIN LSLA
    5 2d42 5.1 5.1 125 249 4 NON-TOXIC CRYSTAL PROTEIN
    6 1z52 4.6 4.4 126 450 9 AEROLYSIN
    7 1pre 4.5 4.2 126 449 9 PROAEROLYSIN
    8 3c0o 4.4 4.2 126 450 8 AEROLYSIN
    9 3c0n 4.4 4.4 126 450 8 AEROLYSIN
    10 3c0m 4.4 4.3 126 449 8 AEROLYSIN

     

    A superposition of BVU_4064 with a top Dali and FATCAT hit, 3g3l, is shown in Figure 1.  3g3l, also a JCSG target (see TOPSAN), is annotated as a putative membrane-associated protein of unknown function from Bacteroides fragilis.  The structures share similar overall topologies, but a significant difference is that 3g3l contains several additional helices at the periphery.

    Figure 1.  Superposition of BVU_4064 (yellow) with 3g3l (blue).

    GS13738A-3g3l-superpose.png

    C-terminal domain:

    Other top structural homologs include 1uyj (epsilon-toxin from Clostridium perfringens) and 1w3g (hemolytic lectin from Laetiporus sulphureus).  These structures share structural similarity to the C-terminal domain, which comprise an extended beta structure; however, their N-terminal domain structures differ and do not overlap.

    Both 1uyj and 1w3g belong to the aerolysin family of beta-pore-forming toxins (PFTs), in which the N-terminal portion of the molecule acts as the targeting domain (carbohydrates in the case of 1w3g) and the C-terminal portion functions as the membrane-inserting and pore-forming module.  Further biochemical analysis will be needed to determine if BVU_4064 may also be a beta-pore-forming toxin acting in a similar fashion.

    Figure 2. Superposition of BVU_4064 (yellow) with (a) 1uyj (red) and (b) 1w3g (green).  The C-terminal domains of 1uyj and 1w3g are structural homologs to the C-terminal domain of BVU_4064.

    (a)                                                             (b)

     GS13738A-1uyj-superpose.png     GS13738A-1w3g-superpose.png

     

    N-terminal domain:

    The closest structural homolog to the N-terminal domain of BVU_4064 is 3e8v, which is annotated as a potential member of the transglutaminase family of proteins (Figure 3), enzymes which catalyze the formation of a covalent bond between a free amine or hydroxyl group and the gamma-carboxamide group of a protein-bound glutamine.  If BVU_4064 is indeed a PFT, however, this domain would more likely function as a targeting domain rather than as an enzyme.

    Figure 3.  Superposition of BVU_4064 (yellow) with 3e8v (magenta), which is a close structural neighbor to the N-terminal domain of BVU_4064.

    GS13738A-1e8v-superpose.png

     

    While the N-terminal domain of BVU_4064 in the structure's current conformation does not overlap with the N-terminal domains of 1uyj and 1w3g (Figure 2), it is interesting to speculate whether or not this domain may be able to flip upwards and away from the C-terminal domain to adopt a similar conformation as those of the N-terminal domains of 1uyj and 1w3g.  It is conceivable that the loop region comprising residues 121-124 (which connect the N- and C-terminal domains) may act as a hinge between the two domains of BVU_4064.

    Residue conservation:

    A ClustalW sequence alignment of BVU_4064 along with its top 6 BLAST hits reveals several regions of residue conservation.  One region is at the N-terminus of the molecule, where ~65% of the first 40 residues are conserved at some level.  This may not be surprising as this region is thought to contain a signal sequence for protein secretion.  A Consurf analysis reveals two regions of conservation at the molecular surface (Figure 4).  In the N-terminal domain, A82, S83, A105, and L106 are quite highly conserved, whereas in the C-terminal domain, A259, H262, G263, H264, G265, H266 are well conserved (residues G267, H268, G269, N273, A274, G275, G276, and G277 are also highly conserved; however, this region of the molecule is disordered in the structure).  It is interesting to note that the conserved region stretching from H262 to G269 consists of several HG repeats; whether or not this is of any significance is unclear.  It may be possible that one or both of these regions in the N- and C-terminal domains may act as the binding region to another molecule/receptor.

    Figure 4.  Residue conservation mapped onto the surface of BVU_4064.

    GS13738A-consurf.png

    consurf_legend.png 

     

    Genome Context:

    STRING analysis reveals that the function of BVU_4064 may involve the outer membrane protein OmpA (protein BVU_4065), which is an ion channel.

    Further biochemical analysis may reveal whether or not BVU_4064 is indeed a member of the aerolysin family of beta-PFTs.  If so, the N-terminal module would most likely act as a targeting domain while the C-terminal module would function in membrane-insertion and pore-formation.

    References:

    Clostridium perfringens epsilon-toxin shows structural similarity to the pore-forming toxin aerolysin.  Cole AR, Gibert M, Popoff M, Moss DS, Titball RW, Basak AK.  Nat Struct Mol Biol. 2004 Aug;11(8):797-8.

    Structural analysis of the Laetiporus sulphureus hemolytic pore-forming lectin in complex with sugars.  Mancheño JM, Tateno H, Goldstein IJ, Martínez-Ripoll M, Hermoso JA. J Biol Chem. 2005 Apr 29;280(17):17251-9.

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    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