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The Open Protein Structure Annotation Network
PDB Keyword
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3l22

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

    Title Crystal structure of SusD superfamily protein (YP_210307.1) from Bacteroides fragilis NCTC 9343 at 2.05 A resolution. To be published
    Site JCSG
    PDB Id 3l22 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS25444,YP_210307.1, BIG_773, 326341
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 4.45 Rfactor 0.146
    Waters
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    Solvent Content 72.39

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3l22

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    Protein Summary

    Gene BF0597 (JCSG target ID 396580, JCSG target accession code PX15618B, GenBank accession code YP_210307.1) encodes a 464-residue long protein from Bacteroides fragilis nctc 9343, a gram negative bacteria that is part of the human gut microbiome.  The bacteria is the most common cause of anaerobic bacteremia (i.e., bacterial infection of the blood) and is commonly involved in peritoneal infections.

    The C-terminal portion of the YP_210307 sequence belongs to Pfam PF07980, which contains RagB, a signalling protein, and SusD [Ref], a membrane protein involved in nutrient binding (Starch utilization System).  The N-terminal portion of the sequence, however, does not match any Pfam as of yet.

    The structure of an N-terminally truncated form of YP_210307 (residues 25-464), solved by Se-Met MAD to a resolution of 2.05 Angstroms, adopts an almost all-alpha fold with four short beta strands (Figures 1). SCOP classifies 3l22 inside the all-alpha class, TPR-like superfamily, SusD-like family.

    Figure 1.  Structure of a monomer of 3l22 (left) gradiently colored from the N- (blue) to the C-terminus (red) and (right) colored by secondary structural elements (helices in blue, beta strands in red, loops in yellow).

    PX15618B-gradient.png   PX15618B-ss.png

    A Dali search using 3l22 as query yields top hits that are all SusD/SusD-like proteins (Table 1).

    Table 1.  Top structural neighbors of BF0597 as assessed by Dali.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3jq1 38.5 2.1 391 464 23 SUSD SUPERFAMILY PROTEIN (Topsan)
    2 3hdx 36.2 2.3 378 456 17 SUSD SUPERFAMILY PROTEIN (Topsan)
    3 3iv0 35.5 2.5 384 466 24 SUSD HOMOLOG (Topsan)
    4 3i4g 34.3 2.3 395 513 22 SUSD-LIKE CARBOHYDRATE BINDING PROTEIN BF1063 (Topsan)
    5 3jq0 33.6 2.3 374 478 21 SUSD SUPERFAMILY PROTEIN (Topsan)
    6 3ck8 33.5 2.5 382 501 18 SUSD [Ref]
    7 3ihv 33.2 2.5 399 535 20 SUSD HOMOLOG (Topsan)
    8 3ck7 33.2 2.5 377 497 18 SUSD [Ref]
    9 3ckc 33.1 2.4 377 500 18 SUSD [Ref]
    10 3ckb 33.0 2.4 377 501 18 SUSD [Ref]

     

    A superposition of 3l22 with several of the top DALI structural neighbors shows that the overall topologies are very similar (Figure 2).

    Figure 2.  Superposition of 3l22 (yellow) with DALI hits 3jq1 (blue), 3hdx (red), and 3iv0 (green).

    PX15618B-superpose.png

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    Ligand Summary

    Reviews

    References

     

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